Continuity mistake: After the scribble creature has been analyzed and found to be made of graphite, the Doctor takes out a pencil and erases some of it to confirm this. The next time the graphite ball is seen, the erased area is gone. (00:14:35)
Continuity mistake: When the Doctor takes a swipe out of a jar of jam in Trish's kitchen and sticks his finger in his mouth, he only has his index finger in his mouth. The scene cuts to Rose giving him a "WTF" look, and when it cuts back to the Doctor he suddenly has two fingers in his mouth. (00:21:15)
Continuity mistake: When Rose grabs the drawing of the Doctor and the TARDIS from Chloe, the upper right corner is bent over rather sharply. In the close-up of the picture as Rose tells the Doctor she'll find a way to get him out of there, the paper is now only slightly wrinkled. (00:30:15)
Continuity mistake: When the Isolus leaves Chloe, in the shot facing Chloe where it says goodbye, Chloe's hand is raised to the wall, where the two were drawing a picture of the Earth. In the wide shot where the Isolus leaves Chloe's mouth, her arm is lowered. In the next close-up of Chloe, when she says "Mum?", her arm is raised again. (00:36:05)
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.