Evolution of the Daleks (2) - S3-E5
Continuity mistake: When Martha is searching for how the Daleks changed the design of the Empire State Building, she is examining the plans for the top of the tower. In the first shot where the new plans are visible, the upper right shows a more detailed picture of a plate of Dalekanium. Seconds later, when we can see the new plans again, it's the same side view but the enlarged picture of the plate with the Dalek bumps is gone. These are still the same new plans (the old plans are on her right) and there was no time or reason for Martha to take another page. (00:24:40)
The Vampires of Venice - S5-E6
Revealing mistake: When the Doctor begins climbing a pillar on top of the bell tower, we can see white sky on the central arch. Two other arches in the very same shot show really dark CG sky. (00:42:17)
Continuity mistake: The Doctor is in a room talking to Amy, Rory and everyone else. He sits at a table where there is a house of cards. The house of cards changes between shots. (00:21:56)
Revealing mistake: When the Editor activates the Doctor and Rose's manacles, the right manacle binding Rose's wrist snaps open as they are shocked. (00:35:12)
Visible crew/equipment: As Sally enters the living room in the abandoned house, in the shot where she walks through the doorway, a cameraman holding the camera can be seen reflected in the window of the door next to her. (00:00:35)
The Impossible Astronaut - S6-E2
Visible crew/equipment: The astronaut coming out of the lake is twice in series 6: In episode 1, "The Impossible Astronaut", and in episode 13, "The Wedding of River Song." In "The Wedding of River Song", when the helmet of the suit is lifted the astronaut is revealed to be River Song. However, in "The Impossible Astronaut", when the helmet was lifted, a man's beard can be seen. Clearly the use of a double to avoid giving the reveal away too early.
Flux: Chapter One - The Halloween Apocalypse - S13-E1
Continuity mistake: At the very start, when Yaz says, "Oh yeah, we are totally in command," just as it begins to zoom out, the handcuff around Yaz's right wrist has the double bar facing out and her left wrist has the single bar facing out, but in following shots both handcuffs are facing the same way. Similarly, this occurs with the Doctor's handcuffs around both wrists, when the Doctor keeps trying the voice recognition. (00:00:10)
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)
The Snowmen - S7-E7
Continuity mistake: When the Doctor offers Clara a TARDIS key, he's holding it differently between shots. (00:44:35)
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: 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 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 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)
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)
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 the Doctor shows Clara the "listen" written on one of his blackboards, the handwriting is different to when it was first shown. (00:07:07)
Continuity mistake: When Craig enters the house and falls back when the cybermat is attacking him, his arms are down by his sides, breaking his fall. As he lands, he's suddenly holding the mouse so it can't bite him. (00:25:51)
Continuity mistake: When the Doctor finds Joe's corpse, he walks up to him and puts his hand on his shoulder. In the next shot, facing Joe, the Doctor is suddenly in a completely different position relative to him, behind him as opposed to next to him. (00:15:06)
The Family of Blood (2) - S3-E9
Continuity mistake: When Sister of Mine enters the school's courtyard after the battle with the scarecrows, her right hand is holding her balloon at the bottom, with the bottom of the string wrapped around her left hand. In the next shot, facing her, her right hand is at her side, with the balloon floating above her left hand. The balloon proceeds to jump between positions until Sister of Mine murders the headmaster. (00:18:00)
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.