Other mistake: After the Doctor tells Bill that Heather's face isn't symmetrical, when he and Bill look into the "puddle" together the Doctor explains that instead of seeing her normal backwards reflection, she's seeing her face "the right way round." The problem occurs in the next shot of the Doctor and Bill seen in the puddle, because the "WOW!" patch on Bill's jacket is properly where it should be, but note everything else is actually backwards. Things such as Bill's color-block top and her denim jacket buttons are on the opposite way. Also note the Doctor's ring has switched hands. Presumably this shot was edited, and the "WOW!" patch was blurred on the left of Bill's jacket then digitally added to the right side, to give the appearance that it's "the right way round" as the Doctor said. (00:20:15)
Continuity mistake: After the Doctor tells Bill that nothing gets through the TARDIS doors, when she responds that they're made of wood and have windows, the Doctor's left hand changes position between shots from being apparently by his side to suddenly resting on the door. (00:28:40)
Continuity mistake: When the Doctor holds out his sonic screwdriver for the Dalek to scan, his grip on it changes between shots. (00:42:25)
Continuity mistake: When Bill says to the Doctor, "Do what you gotta do," he raises his hands to her. His hands are closer to Bill's face in shots facing him than shots facing her. (00:48:40)
Continuity mistake: When the Doctor starts writing "Time" on the chalkboard during class, the "T" is slanted, but in a following wideshot when he's completed the vertical "TARDIS" the handwriting has changed. (00:08:10)
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.