Continuity mistake: When Clara exits the TARDIS in Sherwood Forest for the first time, she closes the door. Shortly thereafter, when Robin draws his sword on the Doctor, the door has opened itself. (00:04:24)
The Sontaran Stratagem (1) - S4-E4
Continuity mistake: In the TARDIS as Donna navigates, the Doctor uses a hammer to help correct the trajectory, then rests it on his neck and shoulder. A second later, when the phone rings, his hand, holding the hammer, is suddenly much lower, below his waist level. (00:03:15)
Continuity mistake: The cab Donna's in passes a red vehicle on the bridge. A second later, it's nowhere to be seen looking back. (00:12:15)
The Impossible Planet (1) - S2-E11
Continuity mistake: When Rose, the Doctor, and the others are running across the walkway a stream of steam appears and disappears between shots. (00:03:55)
Continuity mistake: When Suki goes to leave the lift on floor 500, her arms are by her sides, then suddenly both hands are gripping the strap on her bag. (00:14:00)
The Day of the Doctor - S7-E16
Continuity mistake: After the 10th Doctor marries Elizabeth, they kiss. While they are kissing, the collar on his jacket gets turned up, from her point of view. The camera then switches to look at her from over his shoulder, then back, and now the collar is straight. (00:49:40)
The Day of the Doctor - S7-E16
Continuity mistake: At the end, when the Tenth Doctor steps into his TARDIS, there are three sets of cups and saucers on the side of the bench farthest from the TARDIS, and Clara's set in the middle of the bench, but as the TARDIS fades away, there are two sets on each end of the bench. (01:14:10)
Continuity mistake: When the Doctor uses his sonic screwdriver on the glass partition in the Torchwood Institute, cracks radiate out in a star pattern, meaning the glass will break into pointed shards. When it does break, it breaks into cubes, like safety glass. (00:29:30)
Continuity mistake: When the Doctor is at the Tower of London with Amy and Kate, he claims he needs some air. When Amy follows him she follows him twice, in two different shots. The first time on 'ground view' walking and the second time on 'above view' running. (00:21:20)
Continuity mistake: In the scene where Cobb is briefing his troops, the troops all have their guns, but in the other scene (after you see the Hath marching) the troops are receiving guns. (00:15:45)
Continuity mistake: Throughout this episode, Amy's earrings seem to disappear and reappear.
Amy's Choice - S5-E7
Continuity mistake: When Rory and Amy are running from the Eknodine, there is no mud on Rory's back, but he was thrown on his back into mud a minute before. (00:23:06)
The Family of Blood (2) - S3-E9
Continuity mistake: When Timothy opens the watch into the girl's eyes, Jeremy Baines shouts "Time Lord", then a few seconds later; "What are we waiting for. Attack!" There is then a shot looking down on the scarecrows, Jeremy and Jenny. If you look closely at Jeremy Baines, it's a different actor playing him. (00:16:20)
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: Generally, it seems like it's cloudy on a rooftop, or Atraxi ship is making a shadow on it, but for one moment, after Doctor comes through the hologram, we can see bright sun and a shadow of construction behind the camera.
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)
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.