When Dastan and Tamina jump from the balcony into the fountain below, they are completely soaked. Moments later, as they are taking the horses, both of them are dry.
The completely loaded handle of the dagger represents one minute of time that can be rewound. However, when Dastan refills the dagger, the sand shown in the handle does not reflect 60 seconds' worth of time (it's less than a quarter full, not even 15 seconds' worth), yet the full minute is used up in its subsequent activations.
Throughout the scene in which Dastan and Nizam talk in Avrat, Nizam's cloak continuously changes positions on his shoulders.
While bound to a horse in the Valley of Slaves, Tamina argues with Dastan, and there is a smudge on her right cheek. In the next shot, it has disappeared. Later, it is shown on her other cheek.
When Dastan and Tamina are on the sand dune hiding from the patrol, Tamina can be seen holding the dagger when she stands up. Then Dastan approaches her and produces it from behind his back even though he clearly wasn't ever close enough to have taken it from her.
The letter in the film was written in the modern Persian alphabet (derived from Arabic alphabet), that was not used in Persia before Islam.
The replacement of the Pahlavi scripts with the Persian alphabet to write the Persian language happened in the 9th century.
Dastan was not an orphan, but the son of a local ruler in the southeast of the Persian Empire, who, of course, had a great position and power before the king because of his courage and intelligence.
When Tamina is being readied to be presented to King Sharaman, her maid wipes the henna tattoos, revealing clean skin. Henna paste, once dry, leaves distinctive stains on the skin which take up to three weeks to fade.
When Dastan and Tamina come out of their tent after a massive sand storm, sand has covered everything in sight except for their tent, which doesn't have a single spec of sand on it. Also, not a single spec of sand appears to have gotten inside the tent.
In the second half of the film, two lines of audio play twice. When explaining the importance of the dagger, Tamina says, "The secret guardian temple outside Alamut is a sanctuary, the one place the dagger can be hidden safely," and then, "Give me back the dagger, so that I can take it there." When they reach the temple, the same audio is used, dubbed in while her back is to the camera. The first line has been trimmed to, "The... sanctuary, the one place the dagger can be hidden safely" while the second line is used exactly. You can tell by the intonation of her voice and pacing of her words.
The story is set some 2,500 years ago in the ancient Persian Empire, yet Tamina has shaved armpits.
At the very end of the movie the setting sun moves from right to left, which can only be viewed like that on the Southern hemisphere. The Persian Empire was on the Northern hemisphere. (Either the movie makers used a reversed sunrise viewed from the Northern hemisphere, to make it look like a sunset but forgot to mirror the movie or they did it intentionally showing a sunrise going back in time, which is not completely unlikely since the movie revolves around time travel, but really nothing indicates to that.)
Hashshashins/Assasins (Hassasins in the movie) order was established in Islamic Persia at around 1100 AD. The world in the movie is not yet aware of Islam.
As the Persian army is entering the city, a soldier is carrying a pole carrying on the tip the crescent moon of Islam. If the film takes place in 4-6th century as claimed, this is early by about 400 years. (The moon appears to be a 'smile' as in that part of the world, a crescent moon runs from 9 o'clock to 3 o'clock.)
During the ostrich races, you can clearly see numbers written in modern Arabic numerals on the backs of the riders. This numbering system was still relatively primitive at the time and would not have been stylized in such a modernly-recognizable form.
Tamina mentions the "Mughals of the Hindu Kush" when going into Avrat. The Mughal Dynasty did not emerge till the 14th century, almost a millennium later than when the movie is supposed to take place. It spanned almost the entire Indian subcontinent and was by no means limited to the Hindu Kush mountain range.
The architecture in the film is post Islam architecture and does not fit in with the era of the film, especially the palace in Alamut that looks like a mosque with 4 minarets.
When Dastan is running away from the archers in Avrat's marketplace, you hear Garsiv shouting "Murderer!" When you see Garsiv charge, his mouth is not moving, but sound is still coming out.
During the sand storm, Tamina tells Dastan the story of the gods. Near the middle of the conversation, the camera pans to behind Tamina. Even though she is obviously speaking, her lips are not moving.
The 'Alamut' area is in a mountain area and not desert like in the film; that is why it was so hard to break into it.
Despite what appears at the beginning of the film, Nasaf has never been a capital or royal city of the Persian Empire, either in history or in myth.
Near the end, a Steller's Jay call can be heard. Steller's Jays are North American birds.
Iranian/Persian people speak Farsi. In the movie Arabic words are sometimes spoken by Persian soldiers.
When Sheik Amar talks about his last ostrich Anita, he refers to her as "she", when clearly the bird in the picture is a male ostrich. Male ostriches are black with a white tail, while female birds are greyish brown.