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.
+1, exact same problem.
Ubuntu 18.04.2 LTS, latest updates / upgrades as of today.
DELL XPS 13 9350
Problem started immediately after upgrading to 18.04
logout / login workaround does the trick, but problem comes back every
half an hour or so. So Ubuntu not usable on my beloved notebook :-(
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