Continuity mistake: When the crack in time appearing on the TARDIS' scanner is shown in the "Previously On" segment, the crack is depicted as extending into the leather casing, whereas in the scene in "The Pandorica Opens" where it appeared, it was confined to the screen. (00:00:57)
Continuity mistake: When River is looking at Amy's book about Pandora's Box, her grip on it changes between shots. (00:35:56)
Continuity mistake: When the Doctor and River open the door to the room with the Pandorica and walk inside, River's right arm, with which she's holding a torch, changes position between shots, as does how she's holding the torch. (00:11:04)
Continuity mistake: When the Doctor, River and Amy are exploring, several shots of him are obviously reversed because of the flipped hair part and the fact that he's using the sonic screwdriver in his left hand in them. (00:09:00)
Vincent and the Doctor - S5-E10
Continuity mistake: When Vincent asks Amy "One of my favourite 'whats'?" his right arm is suddenly lowered even though he was just holding up one of his paintings. (00:06:40)
Continuity mistake: When the Doctor takes the piece of TARDIS shrapnel out and looks at it, he's holding it differently between the close-up and the wide shot. (00:44:05)
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)
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)
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)
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)
Continuity mistake: When Liz 10 backs away in pain before asking the Doctor to stop making the Star Whale's screams audible, she raises both her hands in the wide shot, but only has her left hand up in the following close-up. (00:29:31)
Continuity mistake: When the Doctor and Amy are sitting and watching Mandy and Amy is asking what's so important about one girl crying, the Doctor has his hands clasped just below his chin, only for them to jump in front of his mouth in the next shot. (00:08:23)
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)
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)
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 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)
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)
Continuity mistake: When Amy is floating in space outside the TARDIS, her hair is down around her shoulders in the shots of her from above, but floating around her head in the close-ups of her face. (00:03:08)
Factual error: When the shot zooms out from Earth across the Solar System before revealing the narrator, Jupiter and Saturn are shown. Although scaling is somewhat exaggerated, Saturn appears to be closer to the Sun than Jupiter, which it most definitely is not in real life. (00:57:57)
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.