Plot hole: The Brigadier says UNIT HQ is 'a Top Secret establishment'. It is, in fact, so secret that it has a large sign outside informing the world not only of its function, but also the name of the commanding officer.
Plot hole: After UNIT HQ disappears, you can see a patch of grass where the UNIT HQ used to be...but just exactly how can grass grow underneath a building?
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