Interior of Path Determination Glitch

Currently designing some hanzi glyphs, which uses multiple overlapping shapes:

The design features the use of corner components on extra nodes (intersected). Sometimes by moving nodes, on random occasions, the opacity of some outline path glitches (which I presume has something to do with the software determining the interior section of intersected paths), meanwhile the aforementioned corner component glitches and disappears as shown below:

It isn’t that much of a problem since I can get away by nudging a few nodes here and there, but It does worry me if this method is reliable enough before moving on towards more complex glyphs. Hope this glitch can be fixed! Thanks in advance!

Glyphs 3 / Version 3.1 (3133)

Can you send me the file when you find a “glitch”. Then I can try to fix it. Thanks.