Continuity mistake: When the Doctor hands out of the base manuals to the expedition crew for the dream test, Albert Smith is shown with his manual open in shots from behind him several shots before he's shown opening it in a shot facing him. (00:35:56)
The Magician's Apprentice - S9-E2
Continuity mistake: When Colony Sarff arrives at the arena, he's seen unclasping his hands twice, in the close-up and following wide shot. (00:28:38)
The Magician's Apprentice - S9-E2
Continuity mistake: During the exchange where the Doctor says "You flatter me" and Davros responds "A pity. I intended to accuse", Davros' hand goes from just under his chin to resting on his chair's control panel. (00:40:15)
Continuity mistake: At the beginning, Missy is using a knife to sharpen a stick to a point. Later in the scene, when she says to Clara that if they go rescue the Doctor, everything the Daleks can throw at them is between them and him, she lists only the stick among their assets. The knife is never seen or mentioned again after Missy was done with it. (00:04:18)
Continuity mistake: After Missy hooks Clara up to the Dalek armour, she takes her hands away from Clara's temples. However, in shots facing her for the next several shots until she stands up and backs away, her arms are still raised. (00:22:24)
Continuity mistake: Davros' chair has metal parts which go over his shoulders - they are attached to the chair, not Davros. When the Doctor steals Davros' chair they disappear, but when Davros is back in it they have reappeared.
Continuity mistake: When the Doctor is listing questions about what exactly the ghosts are, he goes from gesturing with his left hand in the close-up to gesturing with his right in the wide shot. (00:17:17)
Continuity mistake: For most of the robbery sequence at the beginning, the Nightmare (a disguised Ashildr) is holding her pistol in her right hand. When she's yelling at the Doctor for interfering with her robbery while he's looking at the chest strapped to the back of the carriage, however, she's holding it in her left hand. It switches back to her right after the carriage escapes.
Continuity mistake: When Bonnie is filming the transformation of the Zygon man who she stripped of control over his shape, her grip on the phone she's using changes between shots.
Continuity mistake: When Bonnie throws the laptop with the Osgoods' message to the floor and stomps on it, the computer's position changes between shots - take note of the tape markings on the floor. In addition, the position of the plastic frame of the laptop's screen changes: in the first shot, it's mostly popped out, but in the second shot, it's mostly attached.
Continuity mistake: When Bonnie gets a video call from the Doctor, her grip on the phone changes between shots.
Continuity mistake: When Clara takes Rigsy's chronolock, in the closeup of the tattoo Clara's lifting her hair with her right hand and showing the tattoo with her left hand, but in the next front-facing shot her hands have switched, she's holding up her hair with her left hand and showing the tattoo with her right hand. (00:26:45)
Continuity mistake: When the Shade leaves Clara and she falls, her body is twisted because of the way her legs are bent with one on top of the other and her arms are out to the side. In the overhead shot of her, her positioning has changed, her body isn't twisted and her arms are more straight down her side.
Heaven Sent - S9-E12
Continuity mistake: When the Doctor is first shown discovering the word "bird" written in the sand on the floor of the teleport chamber, the handwriting changes from being somewhat messy in the wide shot to being perfectly neat in the close-up.
Continuity mistake: Rassilon's gauntlet is supposed to be exactly the same one he had in "The End of Time", but the design has changed. Most noticeably, the user's palm is now uncovered.
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.