Continuity mistake: When Amy's dad stands up to present his speech at her wedding, a tear runs down the right side of Amy's face. In the next shot of her the right side of her face is completely dry.
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)
Continuity mistake: After the Doctor says, "Hang on, I missed it!" he smacks his head a couple of times and leaves a red mark on his forehead. When he turns his head immediately after that and says, "I saw," the red mark is no longer there. (00:32:35)
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)
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)
Continuity mistake: When little Amy looks out the window to see what makes the noise, you can see the TARDIS through her window (it's a little blurry) but when you look through the window properly, it isn't there.
Continuity mistake: The Doctor's hairstyle alternates from parted over the left side to a right side part and back while standing by the Pandorica. (00:27:40)
Continuity mistake: When Amy is trying not to forget Rory, the memory of him getting shot does not show the laser blast striking him. (00:41:44)
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)
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: When the Eleventh Doctor is hanging from the TARDIS across London, every wide shot shown shows the TARDIS spinning, but whenever a close-up of the Doctor is shown, the background doesn't spin. (00:00:20)
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)
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: The Doctor's hair changes from the time he realises Rory is there to when the Pandorica is unlocking.
Vincent and the Doctor - S5-E10
Continuity mistake: Amy's tights appear to be gone when she's watching Vincent paint the church. Previously whilst walking to the church they are on.
Continuity mistake: When Rory is telling the Doctor that he can afford to take time off because he just saved all of reality, the Doctor leans against the console twice in two successive shots. (00:51:36)
Continuity mistake: When the Doctor is preparing to seal Amy inside the Pandorica, the shoulder restraint goes from raised to lowered between shots. (00:12:42)
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)
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.