This is a bug with the way the map was built by the nodebuilder, not with the way SRB2 handles the level data. This is Doom--big, open levels were never supposed to exist, and when they do, the format sometimes yells about it!
I highly doubt there's anything that can be done about this issue as, like I said, it's not a problem with SRB2's level handling. (This actually happens on a lot of levels--most of the time it's just not as noticable/is out of the way.)