Revealing mistake: In several episodes of season 9, starting at "Under the Lake" and continuing through "Before the Flood", "The Girl Who Died" and "Sleep No More", the same white hallway model is used. For the first two episodes, this makes sense, since they play in the same location. However, the same hallway is used in "The Girl Who Died", when the men from Ashildr's village get blasted to death, and again in several scenes in "Sleep No More" when the characters run through the hallways. Also, it seems the control room from the underwater research center, where the characters hide from the ghosts in "Under the Lake" and "Before the Flood", is reused as the white room in "Hell Bent" when the Doctor pulls Clara out of her timeline, though in "Hell Bent" the room is nearly empty and the room in "Under the Lake" and "Before the Flood" is full of equipment.
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)
Audio problem: Shortly after arriving at the Drum and taking shelter in the Faraday cage, when the Doctor is looking out the window in the door at the ghosts, he says "What are you?" His jaw doesn't move.
Other mistake: O'Donnell imitates another character retching. The subtitles show this as (WRETCHES). (00:03:00)
Other mistake: Prentis says "In my ship, I have directions to my planet and a selection of items that you can oppress me with." The subtitles say "[...] appraise me with." (00:06:25)
Other mistake: The Doctor says: "He's taking the suspended-animation chamber to the church." The subtitles say "[...] to the judge." (00:15:30)
Other mistake: Clara says "The dark, the sword, the forsaken, the temple." The subtitles say "The Doc [...]." (00:22:10)
Other mistake: The Fisher King says "The Time Lord... Lied." The subtitles say "The Time Lord... Night." (00:35:00)
Other mistake: The line spoken is "You mash up Vikings to make warrior juice." The subtitles say "You must have [...]." (00:12:30)
Factual error: The Viking village has tubs of electric eels in the boathouse, which prove instrumental to the plot as the power source of the makeshift electromagnet used to relieve several of the attacking aliens of their helmets. The problem is that the Vikings live somewhere in northern Europe, and this episode takes place in the 800s. Electric eels are native to the Amazon and Orinoco rivers of South America, which at this point in history no one in Europe knew existed.
Deliberate mistake: In real life, Viking helmets didn't have horns on them, because it would be a liability in combat. The horns were actually for drinking. The Vikings in this episode were given horns anyway, because the writers didn't feel it was worth having to include an explanation of hornless helmets to a general audience.
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.
Factual error: By halfway through the episode, the plot is alternating between following Clara and Jac in London, the Doctor in the fictional Central Asian country of "Turmezistan", and Kate in New Mexico. Despite the three locations being scattered all around the world, only in London is it depicted to be nighttime at any point in the episode. Central Asia and the southwestern USA are both shown to be daytime, despite the two locations being over halfway around the world from each other, and the events all taking place at roughly the same time.
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.
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.