Dark Water - S8-E11
Factual error: When Clara is speaking on the phone to Danny at the start of the episode her phone shows the call waiting screen for an incoming call from him. (00:02:25)
Dark Water - S8-E11
Continuity mistake: When it's revealed that the dream patch is on Clara's hand, it's in her right palm. But in the wide shot when she's getting up as the Doctor explains the true nature of the patches, it's on her left hand instead. (00:13:21)
Dark Water - S8-E11
Continuity mistake: As Clara nods and says "Fair enough" when she thinks the Doctor has told her to leave, her arms go from crossed to by her sides between the closeup and the wide shot. (00:14:29)
Dark Water - S8-E11
Plot hole: When the Doctor and Missy, the latest incarnation of the Master, meet for the first time, she passes herself off as an android. Only later in the episode, after seeing the Gallifreyan hard drive that she has been uploading human minds to, does the Doctor realise that she is a Time Lady, and he doesn't realise that she's the Master until she tells him in the episode's cliffhanger ending. The problem here is that over the show's long history, Time Lords have been shown to have the ability to recognize each other instantly, an ability that makes perfect sense given their powers of regeneration. Previously in the new series, it was even stated that Time Lords can psychically sense each other, an ability demonstrated on-screen in "The End of Time." In "Dark Water", this does not happen, at all. Now, the Master has a history of using technology to block his/her psychic signal before - the Archangel satellite network from Series 3. However, at no point in this episode or the next one, "Death in Heaven", does either the Doctor or the Master even mention such technology as being used, leaving the mystery of how the Doctor didn't recognize Missy as a Time Lady at the very least a rather glaring hole.
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.