Comment 87 for bug 1181666

I switched from gnome-shell to elementary-desktop while waiting for a solution, and the problem disappeared.

So it is really a gnome-shell (or extension or whatever) problem.

To mention: I have the EXACT same beheaviour as the OP, meaning the mouse clicks are not working INSIDE the open windows. But i can still click on items in the Activities screen and the top-bar and still type into already-active textboxes in windows.

I think comments from some people here seem more like a general mouse-click not working problem. Not really sure if these are two different issues or not ...

As i can see it seems a confirmed gnome-shell bug and upstream is working on it: https://bugzilla.gnome.org/show_bug.cgi?id=762193