I've had this happen for a while, originally in GTK3 builds because I was using that, so I was assuming it was a GTK3 issue, but it turns out it also happens on GTK2 builds. Just to be sure this isn't caused by my local build config, I made sure this does reproduce with the latest aurora linux build as of writing this bug. I however don't have a reliable STR. How I end up in this state, though, is that I play videos fullscreen, and that works fine, until it stops working fine for some reason that may or may not involve having multiple windows open, switching windows to other applications, etc. One thing is sure, it's that once I'm in the broken state, I can't even click "Allow" on the full screen popup because that clicks through to the window below. Can't click to seek, can't click anywhere. The only thing that works is key shortcuts, apparently, since I can still hit Escape and come back to the windowed mode. Note that the broken state is not limited to fullscreen videos, although that's how I trigger it, because once in the broken state, the same click-through issue applies to full-screen browser (F11) as well. Also, interestingly, when I have two windows opened, and one of them is in the broken state, that doesn't apply to the other one. Note that my desktop environment is gnome shell, and this may very well be a gnome shell bug.

FWIW, xprop doesn't reveal differences between a full screen window in the broken state and a full screen window in the working state. For example both have: WM_PROTOCOLS(ATOM): protocols WM_DELETE_WINDOW, WM_TAKE_FOCUS, _NET_WM_PING, _NET_WM_SYNC_REQUEST _NET_WM_STATE(ATOM) = _NET_WM_STATE_FULLSCREEN, _NET_WM_STATE_FOCUSED _NET_WM_ALLOWED_ACTIONS(ATOM) = _NET_WM_ACTION_FULLSCREEN, _NET_WM_ACTION_MINIMIZE, _NET_WM_ACTION_CHANGE_DESKTOP, _NET_WM_ACTION_CLOSE, _NET_WM_ACTION_ABOVE, _NET_WM_ACTION_BELOW