Revealing mistake: When the Doctor travels back in time after being shot by the stone Dalek, falls down the stairs and tells himself that he has 12 minutes to live we never see either of the 2 Doctors' faces onscreen at the same time, and if you look at the hair on the Doctor that's dying it is completely different to Matt Smith's. That's because it is Gordon Seed, Matt Smith's stunt double.
Revealing mistake: When the Doctor's jacket is being held by a Weeping Angel while he's monologuing about why they haven't killed him yet, he moves at one point and the Angel's hand moves with him, despite the fact that they're normally effectively stone in situations like this. (00:12:16)
Revealing mistake: When an Atraxi ship appears over the village green, there's a shot where the Doctor, Amy and Rory turn to look at it, and they're standing in bright sunshine with their shadows visible - despite the fact that the Atraxi have surrounded the planet with a forcefield that dims sunlight, so those shadows shouldn't be possible. (00:36:05)
Revealing mistake: In the museum after the Doctor, Amy, young Amy and Rory escape the Stone Dalek, the Doctor uses the Vortex Manipulator to go back in time to tell Rory in 102 AD to let him out of the Pandorica. The third time he goes back, Amy moves despite being dead. (00:19:38)