Continuity mistake: During the sepia-toned explanation of the Doctor and Clara's initial investigation into Sweetville, when they pose as a married couple to infiltrate the place, are accepted, and the Doctor says "The missus and I couldn't be more chuffed, could we love?" in a bad Northern accent, Clara's fake smile goes from closed-mouth to open-mouth between shots. (00:19:57)
Other mistake: When Mr. Thursday goes to see Vastra, to hire her to investigate his brother's death, he doesn't see her face (she's a Silurian "lizard woman from the dawn of time") until she lifts her veil to take a closer look at a photograph he brought her, upon which he faints. However, Vastra's veil is quite see-through, enough that her non-human appearance is obvious to the audience even before she lifts it. The same thing happens when she goes to visit the coroner later - although he doesn't faint.
Revealing mistake: Just before Strax leaves grumbling that he's going to play with his grenades, if you look closely you can see his face mask peeling. (00:27:45)
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.