Journey to the Centre of the TARDIS - S7-E12
Continuity mistake: When Clara asks the Doctor if he's putting the TARDIS on basic mode because she's a girl and he responds "No!", his hand moves from raised to resting on the console between shots. (00:01:39)
Journey to the Centre of the TARDIS - S7-E12
Continuity mistake: In the storage room, when Clara takes a model of the TARDIS down from a shelf, how she's holding it changes between shots. (00:12:10)
Journey to the Centre of the TARDIS - S7-E12
Continuity mistake: When the Doctor begins to explain to Gregor that the TARDIS doesn't actually have a self-destruct, he places his right hand on Gregor's shoulder. In the next shot, his right arm is by his side and he isn't touching Gregor. (00:26:00)
Journey to the Centre of the TARDIS - S7-E12
Continuity mistake: When Gregor hands Tricky the patch from his jumpsuit, Tricky's hold on the patch changes. In addition, the patch is sagging in shots facing Tricky, but not in the close-up of it. (00:32:40)
Journey to the Centre of the TARDIS - S7-E12
Continuity mistake: Before they enter the damaged TARDIS, when the Doctor watches Gregor put down Bram, and then asks Tricky why he's using a blast suit and respirator despite being an android, his hands are clasped in front of his chest in close-ups, but down below his waist in wide shots. (00:09:15)
Journey to the Centre of the TARDIS - S7-E12
Continuity mistake: When the Doctor is asking Clara if she feels safe in the last scene, most of her hair is draped over her left shoulder. However, whether some of her hair is draped over her right shoulder or not changes between shots. (00:45:05)
Journey to the Centre of the TARDIS - S7-E12
Continuity mistake: Near the end, when the Doctor picks up the remote control and reads the words written on it, the position of his hands as he's holding the device changes between the close-up and the wide shot. (00:43:40)
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.