Visible crew/equipment: When the group are thrown into a dungeon in Omega's palace, you can see tape in the corners which is holding the set together.
Revealing mistake: Whenever the TARDIS's scanner picture of the Doctor's laboratory is shown, the TARDIS itself is always in the picture.
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