Plot hole: Yartek tried to disguise himself as Arbitan by wearing Arbitan's robes and pulling the hood over his giant rubber head. Strangely enough, no-one seems to notice that "Arbitan" is now suddenly speaking with a completely different voice, and now has a two-foot-tall-head.
Revealing mistake: In episode one, the Voord that falls down the pyramid shaft is very obviously a cardboard cutout.
Visible crew/equipment: In episode one, when the Doctor is near the pyramid, someone's leg can be seen just before the shot ends.
Continuity mistake: In episode one, Barbara activates her travel dial only seconds before the others. But in episode two, she's been at Morphoton for quite some time - long enough to change clothes, pick fabrics and get food.
Visible crew/equipment: In episode one, when Ian is first seen inside the pyramid, someone stumbles through the background. Some have claimed this is Barbara, but it happens too fast to tell.
Visible crew/equipment: In episode one, when a Voord falls through a pyramid door, a stage hand can be briefly seen on the other side.
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