The Sound of Drums (2) - S3-E12
Continuity mistake: In the conference room, Saxon (The Master) puts on a gas mask that has an emblem mounted above the hose. After replying to the question, he moves the mask, and the emblem is on the bottom of the mask.
Continuity mistake: The Doctor's hair changes from the time he realises Rory is there to when the Pandorica is unlocking.
Vincent and the Doctor - S5-E10
Continuity mistake: Amy's tights appear to be gone when she's watching Vincent paint the church. Previously whilst walking to the church they are on.
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)
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: 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)
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)
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)
Mummy on the Orient Express - S8-E8
Continuity mistake: When Clara tells Maisie that "Difficult people can make you feel all sorts of things", as she finishes the sentence the view cuts from a close-up of her to a wide shot, and the light and shadows cast onto her face change with it. (00:17:20)
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)
Continuity mistake: When the Cyberman in the office locates Clara hiding behind the desk, its gun arm goes from stretched out to bent between shots. (00:00:46)
Time Heist - S8-E5
Continuity mistake: When the Doctor takes the case with the neophyte circuit out of a safety deposit box and opens it, his hands holding the case change position between shots, being suddenly raised higher in the second one. (00:31:27)
Continuity mistake: When Danny is saying "Straight to dinner", the shot switches from one facing him to one facing Clara. In the first shot, Clara is holding up her glass, but in the second shot her glass is suddenly lowered before she raises it again. (00:03:52)
Continuity mistake: When Marian attempts to defend a man who's collapsed from exhaustion from the robot knights, when the knight says "Analysis suggests the peasant-creature is spent", the man goes from sitting up to bent over between shots. (00:17:53)
Continuity mistake: When Colonel Blue informs the team that radiation levels are getting dangerously high as they head for the Dalek's trionic power cells, the team's location inside the Dalek, shown on a computer screen, changes between shots. (00:25:16)
The Time of the Doctor - S7-E17
Continuity mistake: When the Doctor teleports onto the Dalek ship and announces himself, he's holding up a broken Dalek eyestalk in the wide shot as he throws off his hood, but then in the close-up he throws the hood off again, with his arm lowered. Then he raises his arm again, with his arm bent at the elbow, only for a wide shot to have his arm sticking straight up, with his elbow straight. (00:00:55)
The Name of the Doctor - S7-E15
Continuity mistake: When the Doctor pulls the Intelligence's hand off his chin, Simeon's thumb is suddenly no longer touching his face. (00:25:56)
Continuity mistake: During the sepia-toned explanation of the Doctor and Clara's initial investigation into Sweetville, when they pose as a married couple to infiltrate the place, are accepted, and the Doctor says "The missus and I couldn't be more chuffed, could we love?" in a bad Northern accent, Clara's fake smile goes from closed-mouth to open-mouth between shots. (00:19:57)
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)
Continuity mistake: When Skaldak grabs Professor Grisenko's head and announces that Martian law decrees the destruction of the Earth, his hands change position on Grisenko's head between shots. (00:31:47)
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.