On Commons using Safari 8.0.8 I see broken HTML rendering as if partially transparent versions of the Alerts/Messages boxes are overlaying pages (i.e. transparent broken versions of the notification boxes that normally open when you click their icon in the toolbar). Interestingly this only started happening today (Sep 14), does not happen on en.WP, and does not happen in either Firefox or Chrome. It does happen on multiple machines, so it doesn't appear to be a cache or machine-specific issue. I don't see the issue if I am not logged in, but that is presumably because logged out users don't have the alert/message icons.
It's possible this is related to https://gerrit.wikimedia.org/r/#/c/238160/1
Bug is also reported to occur in mobile Safari (presumably in "desktop" layout).