Continuity mistake: At the beginning, when the Doctor takes Amy to planet One, he holds out his hand for Amy to take hold of when they're about to leave the TARDIS. When you see her from the back, Amy lifts her hand wearing her red fingerless gloves. But when it switches shot and faces Amy from the front, she takes the Doctor's hand wearing no gloves. When she steps out of the TARDIS, her gloves are on again.
Continuity mistake: When the Doctor stands between Restac and his fleeing companions, using his sonic screwdriver to disable the Silurians' weapons, as the camera angle changes, the Doctor's grip on the screwdriver switches back and forth between pointing it at the lizards and holding it straight up and down, á la the Neuralizer from Men in Black.
Continuity mistake: When River shows Amy and the Doctor the video of the Angel, next to the Doctor on the ceiling is a bar with two cloth handles, one on each end. The Doctor accidentally rips off the handle closest to him and the viewscreen. A minute later when Amy is alone and we are looking at the Angel video, this handle is back up. It's gone again in subsequent shots.
Continuity mistake: After Prisoner Zero is taken away, when Rory asks the Doctor if everything is back to normal, the Doctor is holding Rory's phone in his right hand while dialing a number. In the shot immediately after, focusing on Rory, where the Doctor walks by him and lightly smacks him on the shoulder, the phone is suddenly in the Doctor's left hand. (00:50:20)skater49th
Continuity mistake: After the Doctor steps through the hologram of his past selves and introduces himself to the Atraxi, in a wide shot, there's a red jacket lying on the ground to the left of Rory. In a close-up of Amy and Rory immediately following, the jacket has suddenly leaped into Rory's arms, to join the other clothes he's holding. When the Atraxi flies away, the red jacket is back on the ground again. (00:53:55)skater49th
Continuity mistake: After the Doctor spits out some yogurt that Amelia gave him and wipes off his mouth, there's still some yogurt on his face and chin. Immediately afterwards, he involuntarily jerks around a bit due to regeneration sickness, and the yogurt is gone. (00:06:35)skater49th
Continuity mistake: At one point while the Doctor is explaining to Amelia what the crack is, there's a shot where he has his hands on the wall examining the crack as he leans over Amelia's desk, then the camera cuts to a shot of Amelia where the Doctor is standing upright with his hands not touching the wall at all. (00:10:15)skater49th