Revealing mistake: In several episodes of season 9, starting at "Under the Lake" and continuing through "Before the Flood", "The Girl Who Died" and "Sleep No More", the same white hallway model is used. For the first two episodes, this makes sense, since they play in the same location. However, the same hallway is used in "The Girl Who Died", when the men from Ashildr's village get blasted to death, and again in several scenes in "Sleep No More" when the characters run through the hallways. Also, it seems the control room from the underwater research center, where the characters hide from the ghosts in "Under the Lake" and "Before the Flood", is reused as the white room in "Hell Bent" when the Doctor pulls Clara out of her timeline, though in "Hell Bent" the room is nearly empty and the room in "Under the Lake" and "Before the Flood" is full of equipment.
The Husbands of River Song - S9-E14
Revealing mistake: When Hydroflax's head is sitting on the section of the TARDIS console with the telepathic circuits, the console is obviously sagging inward, as if made of rubber.
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.