Continuity mistake: When Karra dies and turns back into her human/humanoid form she is wearing a black top that they did not wear as a Cheetah Person.
Continuity mistake: When the Doctor picks up the humanoid skull his hat is looking normal but in the next shot the brim of his hat is folded down and completely flat. In the next shot it's back to not folded again.
Answer: It was never destroyed on-screen; it was intact at the end of the TV movie, and destroyed by the start of the 2005 series. It was destroyed in the novel "The Ancestor Cell," but in a completely different manner to what happened in the series.
DaveJB