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: After the Doctor brings Amy onto the TARDIS, the material of the tweed jacket he's wearing is entirely different in the close-ups of the Doctor's hands, as he's fiddling with the gears on the panel. (00:59:45)
The Time of Angels (1) - S5-E4
Character mistake: When Amy says "Doesn't anybody need me?" from the door of the dropship, there's a misspelling on the door: "Trip Hazzard" instead of "Trip Hazard." (00:16:19)
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. (00:04:54)
The Vampires of Venice - S5-E6
Revealing mistake: When the Doctor begins climbing a pillar on top of the bell tower, we can see white sky on the central arch. Two other arches in the very same shot show really dark CG sky. (00:42:17)
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)
Visible crew/equipment: When Amy is guesstimating Amelia's age, the camera pans to the right and into a crew member's arm. (00:13:49)
Continuity mistake: As the Doctor stares down at young Amy, he takes a perfectly red apple from her and bites it. When the angle changes, and he spits the bite out, the apple has changed to an ordinary red and green one. (00:06:05)
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)
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)
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)
The Lodger - S5-E11
Continuity mistake: When the Doctor is flipping through a book while talking with Amy on his earpiece, in the close-up shot he's using his right hand, but in the wide shot is using his left hand, going through the pages the other way. (00:12:10)
Continuity mistake: When River is talking to the Roman commander after disintegrating a piece of furniture with her pistol, she is shown raising her fingers from the pistol's grip in a shot facing the commander. However, in all following shots facing her, her fingers are still lowered. (00:17:50)
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.