I think that I have found a problem with copying and pasting a certain type of sector arrangement. This example was shamelessly stolen from Null Face to Face.
The stairway with the player start in it is the original, the one to the East is the copy.
The copy was made be selecting all of the sectors in sector mode and pressing Ctrl-C, Ctrl-V.
The stairs all have sloped ceilings as part of their sector properties. For some reason, copying and pasting them messed up the ceiling height offsets. They go from what they were originally set at (each stair has a different value) and they all get set to -95.
One of the originals:
and its copy:
If you load the attached map, you can see the problem in game. The stairs that the player starts at the bottom of are fine but if you go through the little tunnel and look at the other one, the ceilings are all messed up.