After days of fresh reinstallations and tests, I finally found what was
causing this on my end and finally solved it by using a xorg
configuration override 10-evdev.conf as shown on [1]

Offender: Gaming mouse driver (Saitek Cyborg R.A.T.9 Wireless Mouse) 
Driver: libinput

After a bit of research, I found that this mouse is known to be
malfunctioning with the default settings on Xorg. Despite working at a
first look, the default configuration is causing the below symptoms as
explained by [2]

After being plugged, the mouse will seems to work, but you may experience 
different issues :
* You cannot move windows around when grabbing the window's title bar. (happens 
with Openbox and other Window manager)
* You cannot click on buttons.
* You cannot get the focus on windows.
* You cannot open menus, even with keyboard shortcuts.
* Display does not refresh (using Xcompmgr)
* Closing certain windows restores functionality until the mouse locks into a 
new window.

[1] https://github.com/rkruk/R.A.T.-Cyborg-Mouse-on-Linux [working solution for 
R.A.T.9 model]
[2] https://wiki.archlinux.org/index.php/Mad_Catz_Mouse

I hope this helps somes outta there

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https://bugs.launchpad.net/bugs/1181666

Title:
  gnome-shell randomly blocks mouse clicks from working in app windows

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