At the beginning of the episode Amy's fingerless gloves come and go.
When The Doctor, Amy, and River first get to Stonehenge, shots of the Doctor alternate between him with a left hair part and using the sonic screwdriver in his right hand and then with a right hair part and using his left hand. That is, the shots are being mirrored.
A Cyberman is stabbed with a sword which pierced the right door of a two doors, yet when the doors swing open, it's on the left door.
In the last shot, all the stars in the universe are shown to go supernova at the same time. If that were to happen, it would be impossible to see it like that from any one point of view (as long as general relativity holds up) since the stars all have different distances to that point, and therefore the light from their supernovae would arrive at the observer's point in space at different times.
When River is reading out the names of the ships surrounding the Earth, she says Slitheen. While the Slitheen are not a race but a family, River is not listing races but known antagonists of the Doctor, and the Slitheen do fall into that category.
When River Song is talking to the Romans and they have realized she is not actually Cleopatra, space ships fly over and everything shakes, so visibly that the characters all wobble around as though the ground is vibrating. An ornament hanging from the ceiling, however, fails to move even a fraction, revealing that it is, in fact, just the camera wobbling.
When Amy is left to hide behind the Pandorica alone, on her close-up the back wall of this perfect prison wobbles.
When the Pandorica opens and the Doctor says, "The final phase. It's opening." the shot is flipped. The Doctor's hair, which normally flops toward Matt Smith's right, goes toward his left.
River Song successfully impersonates Cleopatra VII Philopator in 102 AD, though Cleopatra died over a century earlier in 30 BC.
On two occasions the cybermen's blue mouth lights are on while the cybermen are not speaking, first when the cybermen are materializing into the chamber and a second time when the doctor is in the Pandorica and its an overhead shot of the alliance.
River states that she's flying the TARDIS perfectly because The Doctor taught her. However in all other episodes she states he didn't teach her, and we later learn The TARDIS taught River.