I have this bug with AnyDesk. Like, disabling AnyDesk autostart
prevented the bug from happening as soon as I logged in, but it would
still happen as soon as I opened AnyDesk (to connect to another computer
or to allow someone else to connect to mine). Whenever I clicked the
invisible square, another AnyDesk window would open. Then even if I
closed AnyDesk the “invisible square” would still be there, but it would
be dead (clicking on it wouldn't do anything, but would block the click
from reaching the window beneath it).

By the way, yes, rebooting or logging out and logging back in fixes the issue 
when it happens, but it's not necessary to go that far. Restarting the shell is 
enough. Here's how:
1. Quit Anydesk (or whichever app triggers this bug in your computer). Make 
sure that it's not running in the background (for AnyDesk, right-click the tray 
icon and close the app from there, so that the app closes and the tray icon 
disappears).
2. Restart the Gnome Shell: hit Alt+F2 to open the “Run a Command” window, type 
the command “r” (yes, just a lowercase letter “r”, without quotes or other 
parameters) and hit Enter.

That makes the bug go away (until Anydesk or another app that triggers
it is started again) without forcing you to close all your programs.
But, as stated, the problem with this is that once you start the app
again the bug will happen again (so once you're done with the app you
have to do steps 1 and 2 above again).

The workaround I ended up adopting was disabling legacy tray icon
support.

The extension I use is “AppIndicator and KStatusNotifierItem Support”,
and I didn't even have to disable it completely; I just had to go into
the options and disable the option “Enable Legacy Tray icons support”.
Just disabling the option does not get rid of the invisible square in
the current session, so if it's already there you'd have to perform
steps 1 and 2 above one last time. Now I can use AnyDesk without getting
that invisible square. One small downside is that the AnyDesk tray icon
doesn't appear anymore, but I can live with that.

-- 
You received this bug notification because you are a member of Ubuntu
Desktop Bugs, which is subscribed to gnome-shell-extension-appindicator
in Ubuntu.
https://bugs.launchpad.net/bugs/2012388

Title:
  X11 window (usually AnyDesk) at top-right of the screen is invisible
  and steals mouse clicks

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https://bugs.launchpad.net/ubuntu/+source/gnome-shell-extension-appindicator/+bug/2012388/+subscriptions


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