The Bells of Saint John - S7-E8
Continuity mistake: When Clara is asleep in bed after the Doctor prevented her from being downloaded by the people in the Shard, he sets up a vase of flowers, a glass of water and a plate of Jammie Dodgers on her bedside table. The positions of the glass, the cookies on the plate, and the torn-open package the cookies came out of is seen when the Doctor leaves a half-eaten cookie on the plate in a close-up. When Clara wakes up, however, the cookies on the plate, the packaging and the glass have all changed positions. (00:19:20)
Continuity mistake: When the Doctor throws his hands in the air and exclaims, "Who da man!?", Rory's phone, which he was holding in the shots immediately prior, is missing. (00:47:25)
Continuity mistake: After Prisoner Zero is taken away, when Rory asks the Doctor if everything is back to normal, the Doctor is holding Rory's phone in his right hand while dialing a number. In the shot immediately after, focusing on Rory, where the Doctor walks by him and lightly smacks him on the shoulder, the phone is suddenly in the Doctor's left hand. (00:50:20)
Continuity mistake: When Amelia comes out of her house with a torch to look at the crashed TARDIS, its exact position in her hand changes between shots a few times. (00:03:30)
Continuity mistake: After the Doctor spits out some yogurt that Amelia gave him and wipes off his mouth, there's still some yogurt on his face and chin. Immediately afterwards, he involuntarily jerks around a bit due to regeneration sickness, and the yogurt is gone. (00:06:35)
Continuity mistake: At one point while the Doctor is explaining to Amelia what the crack is, there's a shot where he has his hands on the wall examining the crack as he leans over Amelia's desk, then the camera cuts to a shot of Amelia where the Doctor is standing upright with his hands not touching the wall at all. (00:10:15)
Continuity mistake: When Mrs. Angelo and Jeff recognize the Doctor, leading to him learning that Amy was known for drawing cartoons of him when she was younger, he keeps changing position between shots. (00:30:05)
Continuity mistake: When the Doctor finds the stolen cup inside Christina's knapsack, he's shown reaching for it twice, in the wide shot and the close-up. (00:38:40)
The End of Time: Part Two - S4-E18
Continuity mistake: When Wilf takes out his revolver and offers it to the Doctor, he's holding it with the grip pointed toward the Doctor. In a wide shot shortly afterwards, Wilf's arm is moving to hold the gun out again, this time with the barrel closer to the Doctor. In the next shot, a close-up of Wilf, the gun is back to its first orientation. (00:25:20)
The End of Time: Part Two - S4-E18
Continuity mistake: When Shaun and Sylvia run out of the Nobles' house to look as Gallifrey begins to phase in and out next to Earth, Shaun's right hand, which he had on Sylvia's shoulder, changes position between shots just before he runs off looking for Donna. (00:40:40)
The End of Time: Part Two - S4-E18
Continuity mistake: When Donna, on the phone with Wilf, is surrounded by Master duplicates in the alley behind her house, she has her phone to her ear, but there's a shot where she looks behind her to see two Masters, one of whom is wearing a bowtie, entering the alley, her phone is missing, only to be back by her ear in the next shot. (00:07:05)
Continuity mistake: After Lucy gets the bottle from the guard, as she explains to the Master that her family had contacts to create something to counteract the "potions of life" used to resurrect him, she starts to take the cork out of the bottle with her left hand, the camera cuts away to the Master and when it cuts back to Lucy, her left hand is on the bottom of the bottle, before she starts to take the cork out again. (00:15:00)
Mummy on the Orient Express - S8-E8
Continuity mistake: When the Doctor offers Professor Moorhouse some jelly babies in a cigarette case, the position of the candy in the case changes between shots. (00:14:10)
Mummy on the Orient Express - S8-E8
Continuity mistake: When the Doctor takes a phone handset from the wall and sonics it before calling Clara, his grip on the sonic screwdriver changes between the wide shot and the close-up. (00:21:45)
Deep Breath - S8-E1
Continuity mistake: In the restaurant basement, while the Doctor and Clara are looking around while speculating on why the clockwork droids are harvesting organs, Clara moves a chain out of her way with her left hand before releasing it, only to be holding the chain again in the next shot. (00:44:10)
Deep Breath - S8-E1
Continuity mistake: After the Doctor walks up to Vastra and Jenny and calls them "the green one and the not-green one", he gestures with his right hand in the direction of the TARDIS. In a wide shot immediately following, he gestures again. (00:03:45)
World Enough and Time - S10-E12
Continuity mistake: After Jorj arrives on the bridge and demands to know which one of the new arrivals is human, the position of Missy's earpiece changes between shots. (00:08:05)
Continuity mistake: After Nardole gets Pictish facepaint, the lines change in consistency and exact positioning several times throughout the episode.
Continuity mistake: When the Captain's arrival at the South Pole is first shown, walking up while Twelve is explaining to One that the frozen snow means something is very wrong with time and asking if either of them is a doctor, to which Twelve responds, "You trying to be funny?", the two Doctors are standing right next to each other. When the Captain's arrival is shown from his perspective, however, the Doctors are standing much further apart when Twelve says the line. (00:09:00)
Forest of the Dead (2) - S4-E9
Continuity mistake: When the Doctor realises that the Vashta Nerada infesting the Library came from the books, he rubs the back of his head with his right hand, with his left hand in his trouser pocket. When Other Dave speaks, and the Doctor turns to him and discovers he's been eaten, he takes his left hand from the back of his head, with his right hand in his pocket. In the shot after that, his left hand is back in his pocket with his right hand in position as if he'd removed it from the back of his head. (00:18:30)
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.