They work fine with zoom at 100% but break at other zoom levels (have tested 90%, 110%, 125%). Mainly tested in Chrome (windows and mac) but I have also tested and seen it in Firefox and Safari as well. I have images and better description posted here: https://phabricator.wikimedia.org/T100952
Topic on Talk:Reference Tooltips
Does this only happen if you zoom in while the popup is currently visible, or also to later popups after you zoom? If only the former, I don't think there's anything I can do. There's no way for javascript to pick up on a changing zoom level so that it can be re-positioned correctly. Sorry.
The latter, this happens after the page is already zoomed. I am usually zoomed in a bit on my mac because the font is a bit small by default, and I see this issue all the time without adjusting the zoom (i.e. it's already at 110% or so).