Continuity mistake: When the Doctor is shown talking to the Daleks on their spaceship, he is standing several metres away. But the people viewing him from Earth see him standing right in front of them. (00:23:33)
Continuity mistake: When the three bride Autons attack Jackie, and they open their hands one at a time, it is clear that when the second Auton opens its hand, all three are already open. After it cuts to Rose, and back to Jackie again, the third one opens (even though we just saw it already open). (00:38:15)
Continuity mistake: At the start when we see Rose on the bus, a bald man sits down on the seat behind her. However, when the camera is inside the bus, he is sitting two seats behind her, without enough time for him to move. (00:00:20)
Continuity mistake: When the TARDIS arrives back from the formation of the Earth, the Doctor and Donna rush out leaving the TARDIS door open. And yet in the very next shot, the door is closed. (00:44:30)
Continuity mistake: When Mickey enters one of the school's computer rooms, dozens of pupils are busy typing, and every one of them is also wearing headphones. However, once Mickey unplugs the main connection for the computers, and shouts for the students to leave, when the students begin to get up, their headphones have instantly removed themselves from their heads and been placed neatly on the desks next to the computer keyboards. (00:36:25)
The Girl in the Fireplace - S2-E7
Continuity mistake: When the Doctor is trying to fix the connection from the past to the future through the fireplace, the background of the spaceship can be seen behind the flames whilst there is no connection. (00:37:15)
Continuity mistake: At the end of the episode, Donna piles suitcases in the Doctor's arms in preparation to leave with him in the TARDIS, and places a striped hat box on top. The bags stay that way for a while as the camera cuts back and forth between them, and you can see the stack of luggage as the camera films the Doctor from behind. Then, as soon as the camera cuts back to the Doctor's face when Donna leaves to give her mother the car keys, suddenly he has one bag under his arm and another in his hand, and the rest of the bags are on the ground with the hat box stacked neatly on top. In addition, when the scene cuts from Donna closing the hatch of her car to her and the Doctor standing by the TARDIS, a large floral-patterned suitcase has appeared, which she was not shown removing from the vehicle. (00:43:15)
Continuity mistake: When Miss Foster uses her sonic device on the window-washer's crane, she points it at the right-side cable, but it's the left-side cable that breaks. (00:26:25)
The Bells of Saint John - S7-E8
Continuity mistake: While Clara shouts, "I don't know where I am," over and over, the Doctor sonics his way into the house. When he kneels beside Clara, then notices the 'girl' on the stairs and stands up, in the shots facing him we can see that the young actress stands on the step facing the stairway (note her legs), with her hand at her side, but in the shots facing the girl she stands facing the door with her hand on the banister. (00:15:22)
The Time of the Doctor - S7-E17
Continuity mistake: After the Doctor yells at Handles for putting him on the Dalek ship, the Doctor grabs him and carries the head with his right arm, then switches the head to his left arm. However, in the close-up as the Doctor asks, "What does this question mean?" we see Handles is back on the Doctor's right arm, but next shot as the phone rings, Handles is carried on the Doctor's left arm again. (00:01:56)
Dinosaurs on a Spaceship - S7-E3
Continuity mistake: At the end Amy and Rory receive a postcard from Siluria with the TARDIS pictured on it, but it is the old TARDIS from 2005 (note there is no St John's ambulance sign on it). (00:46:02)
The Impossible Astronaut - S6-E2
Continuity mistake: When the alien kills Joy in the bathroom in front of Amy, the fragments of her body disappear from the floor once the alien approaches Amy. (00:28:28)
Continuity mistake: When Lawrence is watching the Weeping Angel, just after seeing the Doctor's film/Easter egg, he turns away for a split second. By the time he turns back, you see the Weeping Angel's face only inches from Lawrence's face. But you then cut to a wide shot where you see the Angel's arms outstretched, so its face is about half a metre away from Lawrence's face. (00:34:45)
Continuity mistake: When Mr. Copper is talking about how space-lane fraud could get him ten years in jail, the cut on his forehead changes sides, as does the panel behind him, revealing the shot to be flipped. (00:36:25)
Continuity mistake: When the two Cybermen meet the Dalek for the first time, they are exterminated. They fall directly in front of the Dalek, but when the camera angle changes to show the second Cyberman hitting the floor side on, you can see the Dalek in the background. The Cybermen both fell straight forward, so it shouldn't have been possible to see the Dalek when seeing the Cyberman side on in the next shot, as the Dalek is facing them both directly.
Continuity mistake: When the Cyberman is hit by the electromagnetic bomb, it falls to its knees, then backwards. Yet in the next shot, it is flat on its back, with its leg extended. (00:25:20)
Continuity mistake: When the Doctor first gets on his scooter, we see Rose putting her helmet on before she gets on, but she doesn't do her chin strap up. When we next see her, on the bike, her strap is done up.
Silence in the Library (1) - S4-E8
Continuity mistake: After Miss Evangelista is killed, we see her communicator as her "ghost" slowly fades. In one shot we see from a slight distance the lights left lit tick down to 3, then a short while passes, we cut back and the lights are back to 4. They then tick down to 3 again.
Continuity mistake: When Suki discovers the bodies on Floor 500, she drops her flashlight, but in the next shot she's holding it again. (00:15:20)
Daleks in Manhattan (1) - S3-E4
Continuity mistake: When Diagoras is seen being merged with Dalek Sec, he has gloves on, but when the hybrid Sec emerges, the gloves are gone. (00:45:00)
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.