I think this could be caused by the monitor positions being slightly
weird (none are at 0,0). Although that's not a good excuse and it's
still a bug... Your Samsung monitor is positioned at x=47, y=0 which
doesn't make much sense. Try moving it to 0,0 in Settings or just edit
~/.config/monitors.xml and log in again. Does the bug still occur after
that?

Similarly, an incorrectly advertised work area could be causing the bug,
so please try:

  gnome-extensions disable [email protected]

and log in again.

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https://bugs.launchpad.net/bugs/2113786

Title:
  Dark rectangle over gnome-terminal is a ghost of a "visual alert"

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