I've once had a similar problem in my game where I used ent_createlayer(?) or whatever it is called to create a sky cube in one of the cutscenes. It produced a nexus overflow and showed way too high nexus values in the debug panel. This would lead to subsequent crashes or mostly just weird behavior in following levels, such as unexplainable white surfaces stretching across whole levels - I thought this could be my fault, resulting from ... script errors, I don't know, but they weren't even listed as a regular entity in the level or clickable - or "missing" random models in subsequent level_load calls.
Some stuff regarding the nexus was fixed already, don't know about related or maybe unrelated crashes and errors though: