(at around 52 mins) During the conversation about Brett being a parrot, the length of his cigarette constantly changes.
(at around 1h 35 mins) When trying to abort the countdown, the cancellation instructions Ripley follows with her finger are actually just a French translation of the detonation instructions she followed earlier.
(at around 1h 35 mins) A crewman with a black panel of some kind is visible through the smoke as Ripley runs through the corridors at the end of the film.
(at around 1h 30 mins) The alien's tail snakes between Lambert's feet, but it's not her feet that are shown. Lambert wears cowboy boots; the feet shown wore joggers. The feet and legs were Harry Dean Stanton's (see Trivia).
Jones vanishes from his carrier as Ripley boards the Narcissus. This is deliberate because the fiery explosion effects used would be too cruel to the trapped animal. However, as a consequence, Sigourney Weaver handles the carrier more roughly than Ripley would if Jones was inside.
How did Jonesy, the cat, close the locker door behind him from where he was "hiding" during the initial alien search?
(at around 11 mins) Dallas informs the crew that Mother, the ship's computer, has interrupted their journey having intercepted a transmission of unknown origin, an acoustical beacon that repeats at intervals of 12 seconds. Acoustics is a branch of science dealing with sound. Sound is a mechanical wave that requires a medium, like air or water, in order to propagate. There is none of that in space. However, it is obvious Dallas was referring to the signal being one that was audio only rather than one containing video.
(at around 33 mins) A close-up of the Alien egg when Kane is looking at it shows water droplets falling upwards off the egg, revealing that the shot was done with the camera upside down. (according to Trivia, this is an intended effect by Ridley Scott)
(at around 3 mins) A moving dippy bird toy is shown in the opening scene. Dippy birds require water to work. As the crew is in hibernation and has been for some time, the water in the glass in front of the dippy bird would have long ago evaporated, so the toy would be motionless, not dipping.
When attempting to remove the facehugger by cutting one of its fingers, acid is bled out getting on the gauze, the surgical instrument and the floor but only melts away the floor.
(at around 39 mins) The two holes caused by the facehugger's acid blood in the ceiling of the two different decks have exactly the same shape (re-used shot).
(at around 10 mins) When Parker and Brett are walking through a long hallway and complaining that none of the other crew "come down here", their reflection can briefly be seen in a mirror behind them. Mirrors were used to make the set hallways look much longer than they actually were.
(at around 9 mins) At the very beginning, when Dallas is going through the computer login sequence to communicate with Mother, and all the green-lettered commands are flashing by, the word "ALIGNMENT" is spelled "ALLIGNMENT".
(at around 1h 21 mins) During their fight, just before Ash throws Ripley into a bunk, the camera operator mistakenly knocks the wind chimes. Ian Holm even looks towards the sound, puzzled.
(at around 1h 19 mins) The company's orders received by Mother state, "Priority One - Insure return of organism." Although technically synonymous with "ensure", in common usage "insure" is the wrong verb (suggesting that the company should take out a policy with an insurance company). The statement should be, "Ensure return of organism."
(at around 56 mins) During the chest-burster scene, Kane's shirt is not tucked in during the initial struggle but becomes in when the alien breaks out of his chest (the fake chest).
When Kane, Dallas, and Lambert are in their spacesuits exploring the alien ship, all are wearing white/gray fabric covers on their heads under the domes of their helmets. These are like the "communication carriers" or "Snoopy hats" worn by Apollo and later astronauts. But when Kane's helmet is cut off in the sick bay, no Snoopy hat.
When Dallas is crawling around through the bowels of the Nostromo before he is taken by the alien, you can see a dolly track lining the floor.
(at around 1h 50 mins) In final scene when Ripley uses the grappling hook on the alien. It shouldn't have been able to retract back up because its acidic blood should have melted it away. Unless, of course, the acid was frozen in the freezing vacuum of space (which it was exposed to).
(at around 14 mins) During the landing sequence, Kane issues the instruction "Roll 92 degrees port yaw." Roll and yaw are two separate directional axes. The correct instruction (and what the ship actually does) is "Roll 90 degrees port."
(at around 1h 50 mins) During Ripley's final log entry, she identifies herself as the "3rd officer." She is technically the 3rd in command, or "2nd officer." (Dallas is Captain, Kane is the 1st officer, Ripley is the 2nd officer).
(at around 1h 35 mins) Just after the time limit to override the self-destruction of the ship has expired, the clock starts counting down from 5 minutes to 0. We see the clock counting down and it cuts away when the timer reaches 4:57, and then mother says "ship will self-destruct in T-minus 5 minutes."
(at around 1h 20 mins) When Ripley finds out the truth from Mother, Ash is seen standing next to her. A brief scuffle ensues and Ripley leaves the room. As she leaves there is no injury to her but when the door opens on the other side she has a bloody right nostril.
(at around 1h 23 mins) During Parker's fight with Ash, the sleeve on his right shoulder suddenly becomes torn and a safety pin is visible holding it together. In the next shot we see his shirt intact and we see Ash tearing it.
Burn hole in floor from cutting the Face Hugger appendage is missing when Dallas, Ripley and Ash later search for missing Face Hugger.
In the opening scene, we see the reflection of a computer screen on the helmet with a cup on the right. When we see the helmet again, it is showing a different screen, so the cup is not present.
Mother's two 30 second countdowns take 36 and 37 seconds respectively.
(at around 1h 7 mins) Just before Brett is taken and the alien drops down behind him you can clearly see wires attached to the alien.
(at around 1h 23 mins) After Lambert hits Ash with the electric prod, the camera pans down and we can see wires on the ground leading to the prop Ash torso atop Parker. The torso has no legs, ending at the waist. (Visible in 1979 theatrical wide-screen and full-screen versions, but not in 2003 director's version).
(at around 56 mins) Just after the alien bursts from Kane's chest, you can see 2 steel rods supporting either side of the head. They disappear into the neck when the body is raised high enough.
(at around 1h 19 mins) The computer console refers to an "OVERIDE" instead of an "override".
(at around 1h 21 mins) The milky "sweat" that drips down Ash's forehead before he fights Ripley disappears after he throws her onto the desk. It was not wiped away, because his head is perfectly clean, rather than smeared.
(at around 13 mins) The planetoid where the Nostromo finds the alien spaceship is said to be 1200 kilometers diameter with a surface gravity of .86G. (Earth is 1G.) The horizon would curve visibly on a moon that tiny. By Newton's Law of Gravitation, a body that small would need a density of 50 grams per cubic centimeter to achieve .86G. This is more than twice the density of osmium, the densest element known. It's unlikely that the moon would be made of a massive ball of some hitherto unheard-of, super-dense, stable element. Together, this indicates that the size of the moon is incorrect. (Visible in 2003 director's version, but not in 1979 theatrical version)
Several shots early in the movie where the crew are at their stations the monitor images are projected onto their faces. This is impossible - they would have to look into projectors instead of monitors, so this effect just doesn't make sense.
(at around 1h 22 mins) When Parker is beating Ash with the air tank, the tank bends and wobbles several times as though made of rubber.
Mother's reports of the remaining time in the countdown to self-destruct all say that the explosion will occur "in T minus <x> minutes". In fact, as she is saying that the event will occur after a certain period, the "T minus" is unnecessary. She should simply say that the event will take place "in <x> minutes".
(at around 56 mins) During the "chestburster" scene, Parker is holding Kane's arm when he is convulsing. However, after the alien arrives and Parker has clearly backed away with arms in the air, you can still see Parker holding Kane's arm.
In the takeoff sequence the "entering orbit" announcement is heard just after emerging from the clouds - this is impossible because the atmosphere ends at a much higher altitude than the top of clouds/dust layers, and the orbital speed cannot be reached in air even above a small planetoid, moreover, there must be a horizontal acceleration stage out of the atmosphere to gain the speed necessary for the orbital insertion.
(at around 2 mins) During the introduction scenes of the Nostromo, the stars in the background are maintained even though the spaceship is shown from different angles.
(at around 1h 45 mins) Near the end when Ripley is in the shuttle closet putting on the space suit there are 2 axes hanging on the wall. When she puts the helmet on they have vanished.
Throughout the film, at numerous points, what is reflected in the crew's helmets doesn't agree with what should be reflected.
(at around 1h 50 mins) Because she's no longer in a flight seat or in any way strapped in, when Ripley fires the shuttle's engines, the g-thrust should throw her against the aft bulkhead, but it doesn't.
(at around 1h 14 mins) Just before Dallas is taken by the alien, Ash's headset disappears.
(at around 1h 14 mins) Right before Dallas is taken by the alien he touches a patch of alien slime on the floor. In the next shot he has more slime on his hand than there was on the floor.
(at around 1h 40 mins) Just before Ripley enters the Narcissus (shuttle), she is carrying Jonesy's carrier with the "window" to the front. The next shot shows her holding the carrier with the window to the rear.
(at around 8 mins) When Dallas is first entering Mother, as he passes through the last doorway... when he is seen outside the door, one of the lights on the door-frame is burned out (on his left) but in the next shot, it is lit.
(at around 20 mins) When the members of the Nostromo are exiting the ship to leave to explore the Alien ship,the wind is blowing at high speeds, yet when the steam is shown from the lift it is just drifting down rather than being blown away at high speed. other scenes show the high wind blowing.
(at around 56 mins) When the alien is popping out of Kane, the camera changes angle and there is a significant amount of blood missing from his shirt. Then when the angle changes again, the blood comes back.
(at around 22 mins) When Ripley visits Parker and Brett to inspect their progress, she says "Yeah, you'll get whatever's coming to you." But the word "Yeah" is missing entirely from the soundtrack, and the rest of the sentence is out of sync with the video. This error is not present on the original Alien DVD box set, where Ripley's "Yeah" is muffled but quite audible. But the 2003 theatrical release and the new "Alien Quadrilogy" boxed set both have the word entirely absent.
As the remaining crew members are preparing to leave the Nostromo, Parker and Lambert are trying to deliver additional coolant for the air support system to the escape shuttle. One would expect a real spacecraft's escape vehicle already be stocked with such items and other emergency supplies. However it is made clear that the shuttle is not designed to carry so many passengers for long trips (only two cryotubes are seen inside it, suggesting it can only support two people for a long journey). It is therefore plausible that the crew would need additional supplies in order to survive.
(at around 1h 50 mins) When Ripley comes out of the closet with her spacesuit on in the shuttle to try and get rid of the Alien and she straps herself into the seat the straps are up over her shoulders. Then she scene switches to her fingers pushing the switches and the scene then goes back to her in the seat and the straps are down on her arms. The next time the scene changes again the straps are up over her shoulders.
(at around 28 mins) When Dallas, Kane and Lambert are inside the alien ship containing the space jockey, there is light coming from the left side of the screen, despite them being inside an internal chamber of the derelict spacecraft.
After Ash is decapitated in the fight with his crew-mates, and Ripley reactivates the head to interrogate Ash, the sloppily-edited transition from the prop head to the actor's head is obvious.
When the Nostromo approaches the planet, there is too short time between the phases of the approach - such distances in space would require either much more time or much greater speed - in the latter case the deceleration required for orbital insertion would have lethal effect on the crew.
(at around 1h 19 mins) When Ripley consults Mother, she puts her left hand on a ledge and begins to type with her right. In the close-up she is typing with both hands, but when we cut back to the wider shot, she is still leaning on the ledge with her left.
(at around 1h 30 mins) In the split second shot where the alien drives its tongue into Parker's head, you can see he is bald, but throughout the rest of the movie, he has hair. Also, in a freeze-frame of the shot you can see the alien tongue is white, not airbrushed like the rest of the creature.
(at around 55 mins) When the crew is sharing a meal after Kane regains consciousness, Parker is shown to be talking. The shot changes to show the crew from a closer angle, and although we can still hear Parker speaking, he is shown to be laughing softly and not speaking at all.
The ship's computer, "Mother", deciphers the signal from the derelict ship and determines it to be a warning. However, since this the first time this species has been encountered, it makes no sense for the computer, programmed by humans, to be able to translate the language of a completely unknown species.
(at around 37 mins) When the rest of the crew is watching Dallas and Ash try to get the facehugger off of Kane, Parker asks, "How come they don't freeze him?" but his lips don't move when we hear this.
(at around 56 mins) Blood squib visible during chest-bursting scene.
(at around 53 mins) When Lambert comes to tell the rest of the crew that it will be ten more months until they reach Earth, Ripley is leaning forward listening to her. In the next shot she is leaning against the wall when she says, "Oh God."
(at around 1h 23 mins) After Ash wrestles Parker to the deck, Lambert runs over, grabs Ash (the prop torso) and throws him aside. In the next scene, Ash is still atop Parker. Lambert then hits Ash with the electric prod.
One of the moons in the system containing LV-426 (the target moon) is out of phase with the others.
Just before the alien kills Brett - there is a close up of the alien with dry ice smoke blowing at the aliens head. This is a reused shot from later in the film when the alien kills Parker. The dry ice smoke comes from a pipe the alien broke when it attacked Parker. There should be no dry ice smoke present in the landing leg bay where the alien kills Brett.
(at around 1h 23 mins) When Ash wrestles Parker to the deck, Lambert can be seen dragging Ripley through a hatchway into an adjoining corridor. In the next scene, Lambert is just picking Ripley up. She moves Ripley only a short distance toward the hatch before dropping her to assist Parker.
(at around 1h 21 mins) During the fight between Ash and Ripley, you can see that Ash throws a stunt double, who has bushier hair than Sigourney Weaver.
(at around 56 mins) During the chest-burster scene just before Lambert is sprayed with blood there is a quick shot of alien bursting out of Kane: on a freeze-frame a hole is clearly seen in the table right under Kane's raised hand.
(at around 1h 50 mins) As Ripley blows the alien out of one of the Narcissus' aft nozzles, the engine exhaust is obviously water because it dribbles down the camera. Ridley Scott stated that they used water as a substitute for some sort of plasma. At any rate, there's no reason for the exhaust - whatever it is - to dribble down a camera glass that isn't supposed to be there.
When the first computer screen awakens, and when Ripley calls for a location check, we see/hear that the NOSTROMO has a registration number of 180924609; a second view of a new page on the screen AND in some shots outside the ship show the reg ID as 180286.
Despite the humid temperatures of the ship during the detonation sequence, and the fact that Ripley is seen coated in sweat, including her nails, when she disrobes in the escape shuttle, there is no perspiration anywhere on her under garments, not even the armpits.
During her final transmission Ripley identifies herself as "3rd officer." While she was originally third in command behind Commanding Officer Dallas and First Officer Kane, the deaths of those two placed her in command. She should have more accurately identified herself as "acting Captain" or "Commanding Officer pro tem."
The door to Mother's access terminal makes a noise easily heard over the sound of information being displayed on Mother's terminal. While Ripley accesses Mother, Ash enters the room and sneaks up next to her without any sound heard from the door opening.
When the chestburster erupts out of Kane, Lambert is shown with a terrified/disgusted expression and can be heard saying, "Oh God," when she is hit by the blood spatter but her lips don't move.