Revealing mistake: When the Doctor calls Rose when she is with the Daleks, you can see on the screen of her phone that the call has been going on for at least 57 seconds, but she just answered the call. (00:06:50)
Revealing mistake: In the Torchwood building, a large group of Cybermen start shooting at the Daleks and the Genesis Ark. The Daleks shoot several of them, and you can see a Cyberman that, thanks to hilarious CGI, just collapses like a sock without any physical regard that he is wearing tough metal leg armour, is floating a little off the ground, and falls way too fast than physical laws could allow. (00:25:15)
Revealing mistake: When the Doctor and Rose are talking at the bay, the Doctor's hair is blowing in the wind, but it's not when he is shown in the TARDIS. Considering the image of him on the beach is a projection of him in the TARDIS, the two versions should match. The actor was obviously on the beach recording his lines with Rose and back on a set doing the inside scenes.
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.