The Girl in the Fireplace - S2-E7
Continuity mistake: For most of the scene where he's probing Reinette's mind to find out what the clockwork droids want with her, placing his hands on her temples, the Doctor's left hand is positioned with two fingers on either side of her ear. When he realises that she's seeing some of his memories, his ring finger has jumped to being in front of her ear, without him taking his hands from her head. (00:20:50)
The Girl in the Fireplace - S2-E7
Continuity mistake: When Rose is giving the 5 year warning to Reinette, she's got a noticeable spot on her chin. When Reinette goes behind the tapestry and sees the ship, Rose's spot has suddenly vanished. (00:28:50)
The Girl in the Fireplace - S2-E7
Continuity mistake: When the Doctor is trying to fix the connection from the past to the future through the fireplace, the background of the spaceship can be seen behind the flames whilst there is no connection. (00:37:15)
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.