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.
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)
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 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)
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.