Continuity mistake: When the Doctor is shown talking to the Daleks on their spaceship, he is standing several metres away. But the people viewing him from Earth see him standing right in front of them. (00:23:33)
Continuity mistake: When Amy reassures the Doctor that he stopped the bomb, he goes from leaning on a nearby pillar with his arm completely straight to his arm bent. And then his hand changes position a couple more times. (00:34:32)
Continuity mistake: When Churchill says "KBO" before the Doctor and Amy leave, the cigar he was smoking and just lit is suddenly missing. (00:37:09)
The Time of Angels (1) - S5-E4
Continuity mistake: When the Doctor and Amy are in the museum looking at the Home Box, after they steal it, they run to and enter the TARDIS, which is parked at the end of the hall by the last glass case. However, in the first shots of them in the museum, the camera was pointed directly at that spot, and the TARDIS wasn't there. (00:01:30 - 00:02:00)
The Time of Angels (1) - S5-E4
Continuity mistake: When the Doctor leans on the glass case with the home box, he clasps his hands together. In the next, wide, shot, his hands are separated and in loose fists. (00:01:48)
The Time of Angels (1) - S5-E4
Continuity mistake: When Alistair confronts River, the two guards with him stop and point their guns at her as he walks forward, changing position between the wide shot and the following close-up of Alistair. (00:03:05)
The Time of Angels (1) - S5-E4
Continuity mistake: River's position when she turns away from the door changes between the security playback the Doctor and Amy are watching and the footage shot actually on the ship. (00:03:30)
The Time of Angels (1) - S5-E4
Continuity mistake: When the Doctor is ready to catch River Song, the TARDIS exterior shown is that of the Tenth Doctor's, not Eleven's. In particular, the St John's Ambulance logo is missing. (00:04:35)
The Time of Angels (1) - S5-E4
Continuity mistake: When the Doctor is looking through a hole in one of the pages in the book on the Weeping Angels and River is asking him how early in his timeline this is, which of his hands is on the page changes between shots. (00:17:26)
The Time of Angels (1) - S5-E4
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: When Amy lies down on the tree stump, her hair is all over her face, but on the wide shot her hair is behind her head. (00:12:46)
Continuity mistake: After the Doctor finds out River's in Stormcage, when he pulls out of the pocket computer to look at the readings from the time crack, it rotates in his hand between shots. (00:19:24)
Continuity mistake: In the last scene, when Amy attempts to seduce the Doctor, she pulls his suspenders off his shoulders and he pulls them back on. As a result, the suspenders change position between shots.
Amy's Choice - S5-E7
Continuity mistake: When Rory and Amy are running from the Eknodine, there is no mud on Rory's back, but he was thrown on his back into mud a minute before. (00:23:06)
Amy's Choice - S5-E7
Continuity mistake: When Amy puts on her poncho and says "If we're all gonna die, let's die looking like a Peruvian folk band", the slit changes orientation between shots as she walks to stand between the Doctor and Rory; from across her shoulders to pointing downwards. And no, she doesn't adjust the poncho onscreen to account for this. (00:27:35)
Continuity mistake: When Amy is being pulled into the ground, there's a shot of her arms where the Doctor's hand gripping her left arm is missing. (00:13:38)
Continuity mistake: Throughout this episode, Amy's earrings seem to disappear and reappear.
Continuity mistake: When Ambrose, while standing with Elliott, admits to killing Alaya, in the first shot, Elliott is standing in front and to the right of Ambrose. In the second shot, he's standing to her left. (00:27:52)
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, รก la the Neuralizer from Men in Black. (00:30:30)
Continuity mistake: Near the end, when the Doctor is explaining to Amy that she will forget Rory when the crack in time is finished eating him because he's part of her personal timeline, and he has his hands on her temples, Amy's hair is covering her ears in some shots, but not others. (00:40:56)
Chosen answer: 1) When Stephen Moffat took over he ignored a lot of what had been developed before (there is not in-universe answer). 2) It would have killed Rose, so the Doctor absorbed the energy. His body regenerated before the energy could do a significant amount of damage that would prevent regeneration.