The Impossible Astronaut - S6-E2
Visible crew/equipment: Just after Amy comes out of the bathroom, a boom mic can be seen popping up behind the agent's shoulder. (00:28:55)
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.
The Curse of the Black Spot - S6-E4
Visible crew/equipment: When Amy pulls out a sword before fighting the pirates, you can see a cameraman's reflection on the blade. (00:04:12)
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.