Utopia (1) - S3-E11
Continuity mistake: When everyone is being escorted into the silo after escaping the Futurekind, they all have mud splattered on their clothes - it's especially noticeable with the Doctor, Padra and Jack. Inside the silo, the mud has disappeared. (00:12:20)
Utopia (1) - S3-E11
Continuity mistake: When the Doctor gets the rocket to work by tinkering with the boost reversal circuit, he picks it up with his left hand, sonics it, and then transfers it to his right hand, all in a shot where he has his back to the camera. In the next shot, facing him, he's holding it in his left hand as he pulls something off the device. The shot after that, facing Professor Yana again, the circuit is back in his right hand. (00:18:50)
Utopia (1) - S3-E11
Continuity mistake: When the Master takes the disc with the location of Utopia out of the computer, the exact spot he's holding it changes between shots. (00:40:55)
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.