Revealing mistake: You can see the studio floor in the "white void" outside the TARDIS door in early shots during episode one of this story.
Other mistake: William has a bit of a nightmare, completely throwing the others during one scene by saying the same line ("It's not very likely") twice, and fumbling the line "You knocked both Susan and I unconscious". He also omits the scripted explanation for the melted clocks.
Continuity mistake: Susan's socks disappear during the opening credits.
Audio problem: During Hartnell's big speech about the creation of a solar system, a cough can be heard from off-stage.
Visible crew/equipment: When Susan runs out into the console room in a panic, the shadows of two crew can be seen on the wall.
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