I'm not sure exactly which ones are affected, but possibly more prone when I have multiple source roots under force-app/main.
Happens when rebuilding OST (i.e. spring update).
Im not sure what to do in such case.
Usually I try everything - rebuild OST, remove orphaned symbol table, rebuild caches and indices, invalidate caches, restart IC.
In this case invalidate caches + rebuilding OST helped.
For some projects I just given up and started new one, but it's pretty annoying.