This sort of BSP error ususally occurs when...
You've added and subtracted the same shape multiple times from one location, and/or have too many bsp cuts in one small isolated area of a larger Zone (like a small complex region of a generally non-complex zone).
And it also may be caused if you add a cube to make the height of your floor greater, but the added cube isn't properly aligned or develops a BSP hole, in that case you will fall through to the original floor (I have had this problem when intersecting many spheres to a flat floor to make terrain).
OR...
When the area in question is at the world origin point. This point is represented in Ued by 2 intersecting very dark gray lines. There should be 3 shades of gray for the grid, and the darkest are the world axises. For some reason, you can encounter VERY strange things at the world origin. I have one level where you get stuck at EXACTLY the WO point and no place else. I also have seen BSP errors for no particular reason at this point. Basically the WO is evil.