Other mistake: When Sally is taking the key from the angels, she squats down out of the frame to reveal an angel behind her that has lowered its hands from its face. When the shot cuts back to Sally, there is another angel standing in front of the window on the other side of the room whose hands are also lowered from its face. The two angels with lowered hands are directly across from each other: they should have been frozen in place from this point due to their quantum lock.
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.
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.