Audio problem: When Martha is talking to everyone on her laptop, we can see her mouth moving from the front view. Yet when the camera cuts behind her, she's still talking but we don't see her mouth move. (00:28:32)
The Christmas Invasion - S2-E2
Audio problem: When the Doctor is proving his identity to Harriet Jones by telling her about when they were trapped together at Downing Street, his words don't match the movements of his jaw when we see him from behind - the timing's all off. (00:40:55)
Audio problem: Just after the Doctor makes his appearance and Lynda tells him he's "in the house", she appears to continue talking to him but we never hear what she says; instead the scene cuts to the other two housemates complaining about the Doctor's sudden appearance. (00:01:40)
Audio problem: While Billy Shipton is showing Sally Sparrow the TARDIS (in the room where he keeps the abandoned cars), just after he says, '[You] can't even get in it', he rattles the TARDIS' handle to demonstrate. Watch carefully: When he shakes the handle we hear a rattling noise as if the door is shaking, but in fact the door stays rock solid. (00:19:35)
Audio problem: When the Doctor and Martha are watching Shakespeare in the Globe, Martha says "He's a bit different to his portraits". After she says this on the left of the screen the Doctor's head comes into shot and you can clearly see by his facial expressions he is saying something to Martha, yet no sound is heard. (00:06:10)
The Impossible Astronaut - S6-E2
Audio problem: When the Doctor sits in the Oval Office chair, Secret Service Agents aim their revolvers at him. As they do, the sound of a pistol slide racking is heard. None of them are doing anything except raising and aiming their revolvers at him.
The Wedding of River Song - S6-E14
Audio problem: When Amy says the last two words of "Do you know what else he is, Madame Kovarian?", her mouth doesn't move. (00:34:07)
Audio problem: When Idris/TARDIS says to the Doctor "And you don't care that it's impossible", in a shot from behind them her jaw does not move as she speaks. (00:22:49)
The Vampires of Venice - S5-E6
Audio problem: When Francesco says "Did you just say something about Mummy?", his lips hardly move because of the fang prosthetic in his mouth, revealing that the line was dubbed back in afterwards. (00:39:00)
Evolution of the Daleks (2) - S3-E5
Audio problem: When the Dalek says "Humans will be spared", its ear lights are out of sync with the words. (00:11:40)
Audio problem: Mickey asks Rose why the Daleks are keeping them alive. When she responds, "They might need me," her mouth movements are not in sync with the words. (00:09:25)
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.
A Good Man Goes to War - S6-E8
Audio problem: When Madame Kovarian says, "Give the order, Colonel Runaway," she is seen facing three-quarters away from the camera. Her jaw does not move as she speaks. (00:25:10)
The End of Time: Part Two - S4-E18
Audio problem: During the climax, when the Doctor has Wilf's old service revolver and is alternately pointing it at the Master and Rassilon, there's a cocking sound every time he turns. Not only is the handgun a revolver, so it only needs to be cocked once, the Doctor is only shown actually cocking the gun once, when he first points it at Rassilon. (00:44:10 - 00:45:55)
Audio problem: When the Doctor confronts Mr. Finch/Brother Lassar in the school pool, there is a wide shot of the Doctor from across the pool as he asks Finch, "Who are you?" His mouth isn't moving. (00:23:10)
Audio problem: When Martha says "We're on the Moon. We're on the bloody Moon," her reflection is visible in the window in front of her. Her lips don't move. (00:07:35)
Audio problem: After landing, the Doctor comes out and jumps in place several times. As he does, the sounds of his landings don't sync up with his motions. (00:04:55)
Audio problem: Near the beginning of the episode when we first see Bannakaffalata, he says "Christmas is funny", yet his lips don't match what he is saying. (00:01:45)
Audio problem: When Rose is sitting in the observation deck, after she looks at the tree cutting and suggests they might be related, when she puts it back down, it makes a "clink" sound, as if made of metal, despite being in a sort of cardboard cup. (00:15:20)
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.