Continuity mistake: After the Doctor gets hit in the head by a football, when he raises his arms defensively when Ellie Oswald comes over to see if he's all right, his arms switch positions between the wide shot and the close-up. (00:02:02)
Revealing mistake: While the Doctor and Clara visit the market in Akhaten, the rubber mask of one of the aliens they encounter is revealed, as the eyes of the actor wearing it are very much visible. (00:08:10)
Continuity mistake: The leaf Clara feeds the Old God, which was the catalyst for her parents meeting and which she kept tucked in her book as "page 1", looks completely different to its first appearance in "The Bells of Saint John".
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.