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 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: 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)
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.