Continuity mistake: When Lilith runs her hand along the side of the Doctor's head to distract him so she can get some of his hair, in the wide shots her fingers are extended past his ear. In a shot facing him, however, her fingers are curled and in front of his ear. (00:34:40)
Continuity mistake: When the Doctor is persuading Shakespeare to come up with some words to stop the Carrionites with, in wide shots he has his right arm around Shakespeare's shoulder and is holding his left arm. In close-ups, they are not in physical contact. (00:38:35)
Continuity mistake: When the Doctor first enters Shakespeare's room at the inn, the collar of his coat is askew. The scene cuts to Shakespeare, and when it cuts back to the Doctor his collar is now flat, without him having moved his hands from his pockets. (00:09:20)
Continuity mistake: When Lilith has Shakespeare under her spell and is having him write an alternate ending to his play, there is one shot of his face where his quill can be seen in the corner, perfectly still, even though the next shot shows that he's writing. (00:18:25)
Continuity mistake: When the Doctor, Martha and Shakespeare are in the Globe and they talk about the theatre's architecture, there is a wooden staircase in front of the stage, which Martha and Shakespeare use to descend from the stage when the three leave. Shortly after, at the beginning of the scene where the two actors from Shakespeare's company accidentally summon a Carrionite while practicing their lines, the staircase is gone. (00:22:10)
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.