I am not sure what triggers the issues [complexity of shapes, curves/ straights, number of nodes]. It seems to happen more frequently with fonts. The inside cutouts of letters like B or b or overlapping extensions in handwritten fonts. I have encountered the issue with stock art as well. Those files might have been exported from other tools and got ‘altered’ on the way.
So, before pulling you hair out and wondering why something as simple as a substract is no longer working, try to change the vector orientation. It might be a possible fix to the issue. Good luck!
Eventually, I will write a version of this post for Inkscape – as it has been a common issue in the facebook groups I frequent. Check again in a little bit.