(at around 46 mins) After Harry gets sorted into Gryffindor he goes and sits down next to Ron with Hermione across from him who is sitting next to Percy. In the next shot when Harry asks who's that teacher next to Professor Quirrell he asks Percy and Hermione is sitting to the right of him and Ron is across from him.
(at around 1h 11 mins) When Harry is upside down with the troll holding him by his legs, his hair is pointing to the floor and his scar is no where to be seen on his forehead.
(at around 1h 6 mins) When Hermione corrects Ron's pronunciation of the levitation spell, he had actually said it correctly; it was Draco Malfoy who has said it incorrectly.
(at around 9 mins) When Harry receives his first letter, Uncle Vernon says "Yours? Who'd be writing to you?", Dudley is standing next to him and is seen mouthing Uncle Vernon's lines.
(at around 56 mins) When the students are first learning about brooms, Madam Hooch tells the students to kick off from the ground once she sounds her whistle. She blows her whistle and Neville starts to rise from the ground. Even before he loses control of the broom, she yells at him. He's the only one who did as he was told. Why is he in trouble?
(at around 17 mins) Dudley eats Harry's birthday cake with his hands, but when he turns around, after Hagrid has given him a pig tail, there is no cake or icing on his hands or face.
At the beginning of the movie, when Harry Potter is dropped on the doorstep of the Dursleys (after his parents' death), he is clearly an infant. However, in the album that Hagrid gave Harry at the end of the movie, there is a picture of Harry as a toddler with his parents. If at the beginning of the movie he was an infant when he was orphaned, then it is not possible for him to have a picture with his parents when he was a toddler.
(at around 1h 50 mins) As the three children run across the field to Hagrid's hut, Harry says a few lines ending with "... why didn't I see it before?" Hermione is mouthing Harry's lines with him.
(at around 12 mins) When Harry receives countless acceptance letters from Hogwarts, he fights with Uncle Vernon, saying the dialogue "They're my letters! Let go of me!" Harry's voice is far deeper than the Harry in the rest of the movie, indicating this line was re-dubbed long after main production when Daniel Radcliffe's voice had already begun to change. (Also, his lips are not moving when he says those lines.)
Harry's scar clearly changes positions throughout the movie.
(at around 1h 45 mins) In one scene, Hermione calmly says the word "Voldemort" without the customary flinch or shudder. However in all future scenes and sequels, Hermione is clearly reluctant to say the name and does not overcome this fear until Harry Potter and the Order of the Phoenix. However, as Hermione is Muggle-born and is still young, it is possible she does not yet know the full significance of the name.
(at around 54 mins) When Harry is reading aloud the article in the Daily Prophet about the break-in at Gringotts, he reads words that are not in the article. In particular, he says, "The vault in question, Number 713, had in fact been emptied earlier that very same day." The words "Number 713" do not appear on the page. Harry would have then been unable to connect this to the vault he and Hagrid visited at Gringotts.
(at around 1h 11 mins) When Harry and Ron are fighting the troll in the girl's toilet, they use a spell to lift the troll's club over its head and drop it. The club does hit the troll and makes an appropriate sound effect, but then the club falls to the floor, it makes no sound at all.
(at around 6 mins) When Harry is at the zoo, the snake clearly blinks. Snakes don't have eyelids.
(at around 20 mins) In Diagon Alley, Harry and Hagrid pass many groups of people multiple times, though they appear to be walking continuously in one direction. Watch for the wizard with curly red hair, the man with a top hat and mutton chops, and the group of three girls who cross in the foreground of the opening shot.
(at around 1h 30 mins) When Harry, wearing his Invisibility Cloak, sees Filch looking for him, then spies on Professors Quirrell and Snape arguing, the shots filmed from Harry's point of view have him at eye level with the adults even though he is clearly shorter than they are.
(at around 32 mins) Hogwarts students reach the train by going through King's Cross Station platform no. 9¾, which is secretly located in the barrier between platforms 9 and 10. In reality, platforms 9 and 10 are in separate buildings, and there is no barrier between them, but railway tracks. People wrote to J.K. Rowling about this, and she admitted getting confused between King's Cross and Euston stations. The Platforms actually used in filming are platforms 4 and 5.
(at around 44 mins) In the sorting ceremony scene, Ron goes up to get sorted into his house. After being put into Gryffindor house he runs of in the direction of the tables on the left side of the Hall, even though we know that Gryffindor house table is on the right side.
Owls are very quiet in flight. They have to be, they are hunters and rely on being able approach their prey silently and hear where that prey is in the first place. The owls in Harry Potter - especially in the scene where hundreds of them gather outside the Dursleys' house in Privet Drive - are very loud. Every time they appear, the soundtrack contains loud flapping noises which sounds more like some sort of pigeon than any owl.
(at around 30 mins) Many viewers believe that the infant Harry in the flashback is wearing anachronistic Blue's Clues pajamas. The design on the sleeve is actually a rabbit.
(at around 1h 29 mins) When Harry is in the restricted section, he sets down the lamp to his left before taking off his invisibility cloak, setting the cloak to his right. When Filch's voice is heard and Harry grabs the cloak, the lamp is on top of the cloak and thus falls onto the floor.
(at around 34 mins) The Hogwarts Express only has 4 carriages, so it's not surprising that Ron says that everywhere else is full, so why was Harry alone in a compartment that could seat 6 people?
(at around 1h 3 mins) When Harry, Ron and Hermione just left Fluffy for the first time and walk into their dorm area, we see, under the painting, the feet of someone closing the painting.
(at around 50 mins) When Ron and Harry come into Professor McGonagall's class late and she transforms from a cat into a human, she is not wearing glasses at first, yet they appear on her face as she turns to address the boys.
(at around 8 mins) When Dudley falls into the snake enclosure after Harry makes the glass disappear, when it comes back and Petunia starts calling she is shouting "Dursley" instead of "Dudley".
(at around 35 mins) On the train, the same hill as well as lake (as seen by the waves in the middle of the water) are seen multiple times.
(at around 2h 20 mins) During the end of the film, as the train starts leaving Hogwarts, you can see that Hagrid is a little bit taller than the train. In the next camera shot, Hagrid is shorter than the train.
(at around 1h 50 mins) When Hermione runs across the field her bag switches arms.
(at around 21 mins) Just after passing Madam Malkin's shop and before the owl emporium in Diagon Alley, a woman dressed all in black and a man with a burgundy top hat and mutton chops pass on Harry's right walking in the opposite direction. In the next shot, as Harry looks to his left, the same pair can be seen standing and chatting in the doorway of the owl emporium.
(at around 1h 55 mins) In the scene with the flying keys, we can see the string holding up the broomstick just before Harry grabs it.
(at around 1h 30 mins) When Harry takes Ron to the Mirror of Erised, when Harry drops his cloak and runs away, you can clearly see the lime green from the outside.
(at around 7 mins) When Dudley falls into the snake pit and the glass reappears, by looking at the expression on his face he is calm so we can tell he thinks that there is no glass. He then puts his hand against the window and then gets scared. If he didn't expect glass he wouldn't have put his hand against the window.
(at around 1h 29 mins) When Harry goes looking for a book on Nicolas Flamel in the restricted section he opens up the screaming book to the first page. When the book starts to scream he is in the middle of the book.
(at around 1h 20 mins) During the Quidditch match after Hermione looks at Snape through the binoculars and says "It's Snape! He's jinxing the broom!" you can see Ron mouthing her lines along with her.
(at around 34 mins) Harry and Ron first encounter each other on the platform at King's Cross station, yet on the Hogwarts Express, when Ron asks Harry if he can share his compartment, mountains can be seen out of the windows. This could not be until at least a couple of hours after leaving London. Why did it take Ron so long to find a seat?
(at around 1h 4 mins) The mechanism which makes the Quidditch box shake can be seen underneath the box when Wood falls over after catching the Bludger.
Harry's glasses sometimes have lenses, and sometimes don't, as do Dumbledore's.
(at around 11 mins) When Mr. Dursley is talking about how there's no post on Sundays and the first letter shoots out of the fireplace, the log poker is in the middle of the hearth, when all the other letters come shooting out, the poker is on the right side.
(at around 48 mins) When Percy is taking the first years to Gryffindor Tower, they all seem excited by the idea of moving pictures, even though most of them would have come from magical families and moving pictures would be perfectly normal to them.
(at around 40 mins) When Harry arrives at Hogwarts, Professor McGonagall announces that the Sorting Ceremony will begin "momentarily". In UK English, momentarily means "for a moment" (i.e. briefly), and a Scottish witch as pedantic and precise as McGonagall would never use the American meaning of the word ("in a moment" or "soon"), even though the American meaning might be well understood. Then again, given that the otherwise equally pedantic Snape says "less" when he means "fewer", it could just be that the teaching staff's use of English is just as sloppy as it is in schools all over the Muggle world.
(at around 22 mins) The note that Hagrid gives to the teller in the bank is wrinkled in one shot, neat and clean in the next, and then back to wrinkled.
(at around 52 mins) When Harry is writing down what Snape is saying, the writing is clearly different in the close up shot, than every other time we see the paper, it is much larger and messier whereas in the close up it is small and neat.
(at around 1h 10 mins) When the troll attacks Hermione the first time, its club demolishes the first three stalls. Right before the troll swings its club again, the door of the second stall is still standing.
(at around 1h 15 mins) When the Gryffindor team are walking to Harry's first Quidditch match, behind Harry, in the light, is a girl with blonde hair. But when they are under the wooden shelter she has become a girl with brown hair.
(at around 13 mins) When Hagrid breaks into the Dursleys' island cabin and bends the end of Vernon's shotgun, you can see the white marker where the prop shotgun is supposed to be bent.
(at around 14 mins) In the hut on the rock, when Hagrid comes to fetch Harry, Harry's T-shirt is hanging off his left shoulder at the beginning of the scene, and then it is in the center of his chest, then hanging off the left again, and then back to center.
(at around 37 mins) During the first meeting of Harry, Ron and Hermione on the Hogwarts Express, Hermione's tie changes from being crooked to one side, to straight then back to crooked again.
(at around 1h 55 mins) Ron gets drooled on by Fluffy and gets wet, but two shots later he's completely dry.
(at around 11 mins) When the letters start pouring out of the fireplace, it makes the whole house shake. However, it can be seen that nothing (furniture, wall hangings, etc.,) is actually vibrating.
(at around 58 mins) Before Malfoy throws away Neville's Remembrall, there is no building for a great distance. But after he throws it, Harry catches it right before McGonagall's room.
(at around 33 mins) When Harry arrives on Platform 9¾ the Overhead Line for powering the electric trains is clearly visible above the Hogwarts Express.
(at around 41 mins) Floating candles hanging from visible wires.
(at around 1h 24 mins) When Harry, Ron and Hermione are talking to Hagrid about Fluffy, Ron's scarf goes from being on his shoulder to being draped over his shoulder.
(at around 32 mins) At King's Cross Station, the camera crew is reflected on the left side of the train on the right.
(at around 1h 40 mins) [extended version only] When Harry is reading about Nicholas Flamel on the back of Ron's Dumbledore card, the lime green can clearly be seen where Dumbledore's picture is supposed to be.
(at around 21 mins) In Diagon Alley, when zooming to the Nimbus 2000, the store behind the broom has a blue screen background.
(at around 2h 10 mins) After the final fight when Harry is lying unconscious his hair is thrown back revealing his scar. It has clearly been drawn on with a marker and looks much less real than the wounds on his cheek.
Every car featured on Privet Drive is the same model, the Vauxhall Vectra Estate, which creates an anachronism. This model was made sometime after 1999, which is long after the film was set, in 1991.
(at around 21 mins) In Diagon Alley, Harry and Hagrid walk past the same cart and storefront three times. In the opening wide shot, they walk past the purple storefront with the yellow moving scissors and the cart of market goods in front of it. Three shots later, the storefront and cart are shown again in detail, as Harry and Hagrid pass. The next shot shows them passing the cart (with a stack of cauldrons in the background). Several shots later, after passing the store with the owls, they are seen once again passing the cart with the same stack of cauldrons in the background.
(at around 46 mins) When Harry has been sorted into Gryffindor, he goes to sit next to Ron, opposite Hermione, but when the meal begins, he is sitting next to Hermione. He is also on her left-hand side, away from the top table; this would imply that he was sorted before Hermione, instead of afterward.
(at around 44 mins) When Harry sees Snape in the Great Hall during the sorting ceremony, we can see the back of Professor Quirrel's head. Quirrel's hair is clearly visible under his turban despite the fact that Voldemort's head would be here. It is gone when Voldemort is revealed.
(at around 13 mins) When the shotgun blast from Vernon's shotgun goes off he only pulled the trigger one time. But when the hole in the ceiling is seen there are two partial holes seen side by side. A double-barreled shotgun has two triggers so that the blast doesn't knock the shooter back on their rear end. Therefore there should only be one hole in the ceiling.
(at around 1h 1 min) When Harry, Ron, and Hermione are walking up the stairs and the stairs are changing, you can still see the banister wobbling back and forth even after they've reached their final position.
(at around 10 mins) When Harry peers out from under the stairs Uncle Vernon is screwing a board over the mail slot. The board in this shot runs from the upper right of the screen to the lower left. But in the shot when the letters start flying into the house the board is positioned from the upper left to the lower right.
The number of place settings at the tables at the initial feast show that there are 8 first-years in each house, which would make 32, but when the pupils are lined up for their first flying lesson, there are only 26. However, it's perfectly reasonable to have extra place settings at the house tables - regardless of the total number, it isn't known how many first-years will be seated at each table until they are sorted.
(at around 4 mins) When Harry wakes up in the beginning of the movie his shirt is tucked in the back of is trousers. In the next shot it is not.
(at around 2h) During the chess scene when the chess pieces are being destroyed, the bits of rubble can be seen flying in opposite directions and sometimes even just a split second before the actual piece is destroyed.
Hagrid picks Harry up on his birthday, 31st July. He takes him to the train station to set off to Hogwarts the next day, even though term doesn't start until 1st September.
(at around 40 secs) In the very beginning of the movie, Dumbledore is walking towards McGonagall who is still in cat form. As he is walking, you can see his shadow cast against a backdrop of trees.
(at around 1h 12 mins) In the scene following the defeat of the troll, Quirrell is shown speaking with the other professors, at which point they, and the trio, leave the girls' bathroom. Their footsteps are clearly heard as they move down the hall; however, in the next shot of the troll laying on the floor, the sound effects have ceased. In the last shot, of Quirrell jumping nervously in response to the troll grunting, the footsteps can again be heard.
(at around 2h) In the chess sequence the White (enemy) Queen is shown destroying 2 separate Black Rooks, but as Hermione took the Queen side castle there would only be 1 Black Rook piece in play. It is possible that a pawn was promoted but as it is shown on screen that Black (Team Ron) loses their Queen they would likely replace it with a Queen making this unlikely.
(at around 2h 5 mins) At the end of the chess match, Ron is supposedly knocked unconscious. When Harry and Hermione run to check on him, Harry touches Ron's arm and Ron's mouth twitches.
(at around 35 mins) Twice in the film, the British word "bogey[s]" is spoken: once when Harry and Ron meet on the train, and once at the end of the troll scene (at around 1h 12 mins). On the American DVD, the subtitles transcribe this as "booger[s]", a synonym which sounds very different.
(at around 11 mins) When the multiple letters fly into the house from the fireplace, Harry catches one out of the air and it is obviously a single sheet of paper rather than a stiff envelope like the first one that was delivered and opened.
(at around 9 mins) When Uncle Vernon is ripping up the letters that come through the mail slot, you can see that the envelopes had already been cut, making it easier for him to rip up.
(at around 34 mins) During the train journey, Ron's hair is parted in several different places.
(at around 2h) In the chess sequence, Harry is shown on a3 as a Black Bishop when Ron moves to h3 to check the King on g1 before being taken by the Queen on c3. Given that Harry moves to check the King his only possible move would be to go to c5 which would not be checkmate, making Ron's sacrifice in vain as the King is free to move to f1 or g2 since Hermione is on h8. A cheating spell may have been employed.
(at around 1h 35 mins) Hagrid tells the trio that Professor Snape helped put forth protections over the stone; therefore, he could not possibly be trying to steal it. However, Snape's contribution from the book - a logic puzzle involving a number of different potions - was left out of the film and not given a replacement, making Hagrid's statement invalid.
(at around 1h 1 min) When Harry, Ron and Hermione first enter Fluffy's corridor, and start running towards the door, one of the torches clearly has a little flame, before it 'bursts' into flame when they pass it.
(at around 12 mins) When Vernon chases after Harry when the letters are coming into the house, you can clearly see a crack in the wood covering the mail slot just before the letters burst through.
Although moving and talking portraits are a hallmark of the Harry Potter universe, not all wizarding portraits are like this. We see many ordinary, non-moving portraits at Hogwarts throughout the film.
(at around 28 mins) After Harry has received his wand in Ollivander's, his hair is parted to show his scar. However, when Hagrid knocks on the window and Harry sees Hedwig, his scar has mysteriously disappeared.
(at around 35 mins) After Harry has bought the contents of the sweet trolley on the train, an exterior shot shows that the sun is still fairly high. Hermione then joins them, and tells the boys that they had better change into their robes as they will be arriving soon. Yet when the train pulls into the station it is at night.
(at around 40 mins) When the first years climb the stairs and meet Professor McGonagall for the first time, Ron's robe is hanging partly open in one shot, but is closed in the next.
(at around 5 mins) When Harry and the Dursleys are getting into the car before going to the zoo, Vernon is seen speaking to Harry. From the backside, Harry's button up plaid shirt is seen on his shoulder, then from the front it is hanging off his shoulder.
After escaping from the Devil's Snare, Harry, Ron, and Hermione all have dirt stains on their faces and clothing (from landing in the dirt beneath the plant). The amount and placement of the dirt stains vary from shot to shot throughout the finale, and in some shots seem to disappear entirely. This is most noticeable on Hermione's tights (the white provides a strong contrasting background for the dirt).
Harry receives several small facial wounds and rips in his sweater in the key room. During the subsequent chess match, the size and placement of the wounds and rips vary from shot to shot.
(at around 51 mins) When Snape first enters his classroom, he bursts into the room and the door slams open. The actor who is sitting in the front row on the right continues to look at the door well after Snape has made his way to the front of the class, as if expecting the door to close. He also does a double take during this time.
(at around 54 mins) There are two articles on the front page of the Daily Prophet about the break-in at Gringotts. The article below the headline story, starting with the line "the vault in question had in fact..." is identical to the top article.
(at around 2h 10 mins) Near the end of the film, just after Quirrell ignites the surrounding flames, Voldemort says "Don't be a fool. Why suffer such an horrific death..." This is, in fact, incorrect. The correct term would be "Why suffer such a horrific death". Actually, the an rule applies to H-words since it often creates a vowel sound.