I have this problem too. 
The real problem for me is less  the dots staying in place, but alt-tab not 
working anymore.
With so many people being affected - did anybody find a workaround other than 
not using wayland or logging in and out?
Is there anything people not deeply into Gnome and/or thunderbird development 
can do to help it getting solved?

I tried to kill and get gnome-shell reloaded, as I used to to before
sometimes, but that just leads to the whole gnome-shell going down and
not coming up again, as far as I understand this is related to using
Wayland, where killing gnome shell and having it restart automatically
seems not to be supported.

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Ubuntu.
https://bugs.launchpad.net/bugs/1932328

Title:
  Thunderbird under Wayland does not correctly close (or manage) windows

Status in Mozilla Thunderbird:
  New
Status in gnome-shell-extension-ubuntu-dock package in Ubuntu:
  Confirmed
Status in thunderbird package in Ubuntu:
  Confirmed

Bug description:
  Using Ubuntu 21.04 (Hirsute) that starts in Wayland, by default.
  Thunderbird version: 78.11.0 with "gnome-support" package.
  Same problem in safe mode.
  Description:
  By default in this context, TB is a Wayland task.
  When opening a compose windows (or reply or transfer), sending mail 
apparently close the windows, but gnome shell continue to show multiple 
"points", as if multiple windows are still active.
  And after closing TB, it seems maintained in the same state, so it becomes 
impossible to relaunch it from the desk. But task manager of "looking glass" 
does not show it and it is possible to launch from terminal.
  Provisional solution:
  Modify .desktop file to launch with --display=:0 option, that force to use 
XWayland interface, as shown by xlsclients (for example).
  But it is actually a bug under Wayland context, that also badly interfer with 
many add-ons or extensions.

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