Continuity mistake: In this episode part of the TARDIS set was erected incorrectly, resulting in some of the roundels emerging from the wall rather than being indented into it. This is very visible in all the TARDIS 'console room' shots.
Continuity mistake: In episode 4, approximately 5 minutes from the end of the story, Soldeed is shot after he pulls the lever that sets the complex on overload, and then crumples to the ground dead beneath the lever. Then, after the Doctor and everyone else get out of the complex, we see a selection of shots taken inside the complex - one of which is the room with the lever that Soldeed pulled, except he's no longer there...
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