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I get this with a VIS compile, and cordon compiles, both with and without vis.
I have a hint brush not included in the cordon compiles, and 4 instances of the pwindow_01_med prefab. I'm not sure what's causing this, but if it's the prefabs, it can be fixed easily.
Can anyone tell me what the error means outside of the literal sense and how to fix it?
EDIT: I fixed it.
Note to anyone getting this error: Look for areaportals on multiple sides of an area; My problem was that I had 2 sets of windows, and the portals were on both the front wall and the one beside it, which made the engine stop working.

If you use Valve's window prefabs, make sure they're only on one wall in a visgroup, or delete the func_illusionaries and areaportals.