Continuity mistake: The scene where the Doctor forces Jex over the boundary line starts off in roughly mid-afternoon lighting, but when the Gunslinger arrives and Isaac is shot, the sunlight is at a much lower angle. (00:25:35)
Continuity mistake: When Amy and the Doctor are arguing over whether Jex should be punished, her hair is blowing a lot in shots facing him, but very little in shots facing her. (00:24:10)
Dinosaurs on a Spaceship - S7-E3
Continuity mistake: After Rory and Brian are sitting in the control chairs, when the Doctor makes a Silurian joke and then gripes that no-one found it funny, Brian's hands move to the buttons on the end of the armrests instantaneously between shots. (00:39:20)
Dinosaurs on a Spaceship - S7-E3
Continuity mistake: When the Doctor notices Brian and starts questioning him on how he got aboard, he's shining his flashlight into his face, but then the light is gone in a close-up of Brian. (00:03:01)
Continuity mistake: When the Doctor reaches up to touch the face of the woman he's meeting, his left hand, with which he'd just grabbed the woman's hand in the previous shot, is by his side, only for him to be holding her hand again in the next shot. (00:01:57)
Continuity mistake: When Rory pulls out his torch and starts looking around, it switches hands between shots. (00:17:43)
The Doctor, the Widow and the Wardrobe - S7-E1
Continuity mistake: When the Doctor asks the wooden people to show the Arwells where the timeship is going, the queen raises her hand, widening the window's field of view. In a shot shortly after focusing on the Doctor, the queen's hand is lowered in the background, before suddenly being raised again. (00:48:57)
The Doctor, the Widow and the Wardrobe - S7-E1
Continuity mistake: When the Doctor starts falling towards Earth with the spacesuit, the planet is noticeably smaller than it was when the spaceship he's falling from was arriving above Earth at the very beginning. (00:01:33)
The Wedding of River Song - S6-E14
Continuity mistake: When River sits down by the table as she and Amy are talking and drinking wine, in shots of River, Amy's wineglass is sitting on the corner of the table. In shots of Amy, the glass is first absent, then Amy reaches over, grabs it and takes a sip before resting it on the table with her hand holding the stem, whereas her hand is in her lap in shots of River. (00:40:40)
The Wedding of River Song - S6-E14
Audio problem: When Amy says the last two words of "Do you know what else he is, Madame Kovarian?", her mouth doesn't move. (00:34:07)
The Wedding of River Song - S6-E14
Continuity mistake: When the Doctor realises he's picked up a model of the TARDIS in Amy's office, it rotates in his hand between shots, as indicated by the positioning of the sign on the front door. (00:20:55)
The Wedding of River Song - S6-E14
Continuity mistake: During the live chess game, the position of Gantok's hand changes between wide shots and close-ups of the electrified queen piece. (00:06:33)
Continuity mistake: When the Doctor overhears Alfie crying while stirring something in the kitchen, he has the spoon in his hand in the close-up, but his hand is suddenly empty in the wide shot. (00:23:02)
Continuity mistake: During the Doctor's phone conversation with Rita, the handset of her phone keeps switching between ears. (00:32:30)
Continuity mistake: When the Doctor tells Howie that he should continue telling himself the situation is a "CIA thing", he puts his arm around his shoulders twice. (00:11:22)
Continuity mistake: When Rory brings the unconscious Amy inside the TARDIS and puts her on the floor, the Doctor drapes his jacket over her twice. (00:39:44)
Continuity mistake: When Purcell is sinking into his carpet, just after a shot where he's shown having sunk into the floor up to his waist, we see a shot focusing on his dog where Purcell's legs are visible as he falls forward onto his hands, despite his legs having already been pulled under. (00:23:38)
Continuity mistake: When the Doctor is talking to the Voice Interface Amelia, when he starts saying that "Scotland's never conquered anywhere, you know, not even a Shetland", his left arm, which was stretched out along the railing in the previous shot, is suddenly lowered. (00:27:28)
Revealing mistake: When River grabs a gun off one of the soldiers she just knocked out with regeneration energy, the actor sits up slightly, even though the soldier is supposed to be unconscious. (00:24:44)
Continuity mistake: When the Doctor is talking to the Amelia voice interface, in a shot of him from behind his position slumped against the railing is different from shots of him from the front. (00:27:37)
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.