Oh if you could find a way to replicate it in the most simple way that is extremely helpful.
The first thing I would try, is to delete everything except the pupil, iris and the bones that control them.
Then remove any GP layers that aren’t used anymore so it’s just what’s used.
If it’s still present, then you rebuild this thing from scratch (the simple version) and see if it happens in the latest version starting from nothing.
That’s when you know you’ve isolated the bug and it isn’t caused by anything weird in the older file.