From the various issues on spellcheck it seems that Scintilla has a problem drawing indicators on damaged or zero width characters.
The fact that @eht16 can't reproduce suggests its also font and/or Pango version dependent. @hroncok as I keep saying, post the version of GTK and Glib and OS and version (see top of help->debug messages) and also the font and size you use, and @eht16 too :) @hroncok can you try different fonts and sizes?
Maybe it needs to be pushed upstream, but since this is the no longer supported Scintilla 3 the answer is likely to be try Scintilla 4?