Probably caused by rGVED8ec804988d59: Make sure the toolbar is shown on top of surface contents even when not floating (https://gerrit.wikimedia.org/r/#/c/359033/), which set z-index: 2 on the toolbar. We can't lower that to 1, otherwise the toolbar (when floating) will be overlapped by context menus and such.
I suppose we can just raise z-index on div.vectorMenu div.menu from 1 to 2? It shouldn't cause any problems, but it sucks a bit for VE to require CSS fixes in skins.
Or we could make .ve-init-target into a new stacking context (e.g. position: relative; z-index: 0; ref), so that z-index values inside of it don't "leak". That feels neater, but I have no idea if it's likely to cause further issues. Ed, thoughs?
(Side note, I found some weird CSS on en.wp when looking into this, see https://en.wikipedia.org/wiki/MediaWiki_talk:Vector.css#Remove_.22Menu_over_FR_box.22_rule)