Continuity mistake: When Amy is being pulled into the ground, there's a shot of her arms where the Doctor's hand gripping her left arm is missing. (00:13:38)
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)
Continuity mistake: Throughout this episode, Amy's earrings seem to disappear and reappear.
Plot hole: When the Doctor realises that something is coming up from below ground, he tells Nasreen and Tony that at the speed the three transports are coming, the underground arrivals will reach the surface in 12 minutes. The rushed preparations that ensue, including hurrying from the drill hall to the old church and setting up a surveillance network outside, couldn't have taken less than 12 minutes to set up, especially given that they also had to: inform the others trapped inside the shield (Rory, Ambrose and Elliot), inform Rory and Ambrose that their significant others (Amy and Mo) were missing, run between the old church and the block of houses and gather supplies. And, lest we forget, there's also Rory and the Doctor arguing about what happened to Amy and Ambrose's initial skepticism as to what is occurring.
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.