Visible crew/equipment: As the black suited figure stops to look at Martha, the crew and equipment are reflected in the helmet and visor. (00:02:30)
Visible crew/equipment: After the acting Prime Minister gives orders to the sergeant and the lift doors close, the soldier turns around. As he issues orders, the boom mic is reflected on his goggles. (00:05:25)
Visible crew/equipment: As the Doctor tries to get Donna to jump to the TARDIS, as the camera is in a close up on her in the taxi, the yellow camera vehicle is reflected on the cab's paint. (00:12:50)
Visible crew/equipment: On the Moon's surface, the camera and boom mic can be seen reflected on the visor of the astronaut as she talks to Clara.
The Sontaran Stratagem (1) - S4-E4
Visible crew/equipment: As the Doctor tries to get Wilfred out of the car, the camera goes to follow his movement and there is a reflection of the lighting rig and camera on the car.
Visible crew/equipment: As Sally enters the living room in the abandoned house, in the shot where she walks through the doorway, a cameraman holding the camera can be seen reflected in the window of the door next to her. (00:00:35)
Visible crew/equipment: When Rose and the Doctor are riding after landing, you see the camera, crew and lighting equipment reflected in their glasses. (00:04:00)
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.
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.