maybe: https://github.com/Wiwiweb/FactorioMilestones/pull/25
Hi there! Stumbled upon this and thought I'd dig a little into it just for fun.
This only happens if you add an item in a different quality that you already reached the corresponding normal quality milestone for, right? When you add a quality milestone for an item you haven't reached the normal milestone yet, all is fine? You would have to have reached the normal one afterwards of course, to see a difference, so you probably didn't.
However, if I haven't missed something, I think the PR seems to fix it. When adding a milestone, the mod checks whether it has already been reached before, which makes sense, but that check doesn't seem to consider quality.
If you feel comfortable with it, you can edit the file in the mod's zip on your machine, it's just one line, and see if it works; might be valuable feedback, and if it works, you wouldn't have to wait for the PR to be approved back into the mod's repo.
Of course, no guarantee that it doesn't mess up something else, I'm not familiar with modding Factorio...