The Curse of the Black Spot - S6-E4
Continuity mistake: When the TARDIS starts shaking ominously while the Doctor and Captain Avery are onboard, the handle of the big starting lever on the console moves between shots. (00:18:03)
The Curse of the Black Spot - S6-E4
Continuity mistake: When the pirate whose hand Toby cut pulls his gun on the kid while Toby is pointing a sword at him, when Mulligan grabs the keys from the other man's belt, the positions of the weapons change relative to each other. (00:18:20)
The Curse of the Black Spot - S6-E4
Continuity mistake: As the Doctor explains that the TARDIS is headed for a "full-on screaming tantrum", the lever his right hand is on moves between shots, and he's not shown pulling it. (00:18:40)
The Curse of the Black Spot - S6-E4
Continuity mistake: When the Doctor is telling Amy that they have to release the Siren, his hands on her collar change position between shots. (00:30:05)
The Curse of the Black Spot - S6-E4
Continuity mistake: The pirate that Toby cuts on the hand with a sword in order to make him stay in the magazine is gone when the Doctor and Captain Avery return, but reappears on the spaceship at the end with the rest of the crew.
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.