This seems to be something to do with the version of the dash under
mantic, and with the fact it's running under Wayland specifically. A
similar issue came up on the Pi forums, and included an excellent
minimal reproduction case (which I'll include here for simplicity).
Notably, the issue does *not* occur (with either this reproduction case,
or with quassel) under Xorg, only under a Wayland session:

~/.local/bin/stopwatch:

  #!/bin/bash
  echo "STOP"
  echo "Watch"
  read

~/.local/share/applications/stopwatch.desktop:

  [Desktop Entry]
  Version=1.0
  Type=Application
  Terminal=false
  Icon=StopWatch
  Name=StopWatch
  Exec=gnome-terminal --class=StopWatchTerminal -- 
/home/ubuntu/.local/bin/stopwatch
  StartupWMClass=StopWatchTerminal

Adjust the /home/ubuntu/ path as necessary. Pin the "StopWatch"
application to the dash and launch it; under Xorg a dot appears next to
the pinned application. Under Wayland, an additional "gnome-terminal-
server" icon appears on the dash.

-- 
You received this bug notification because you are a member of Desktop
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Ubuntu.
https://bugs.launchpad.net/bugs/2044382

Title:
  Quassel opens "another" icon under Gnome

Status in gnome-shell-extension-ubuntu-dock package in Ubuntu:
  New
Status in quassel package in Ubuntu:
  New

Bug description:
  I'm unsure if this is a bug in quassel, or in the gnome dock itself.
  Under Ubuntu 23.10 (mantic), running Quassel from a pinned icon on the
  left bar results in the pinned icon appearing "idle" (not running),
  and a second icon appearing below those that are pinned which
  apparently represents the running quassel instance.

  Pressing the idle quassel icon (or pressing the Super+4 shortcut for
  it) runs *another* instance of quassel rather than switching to the
  running instance. The "extra" icon also cannot be pinned (and
  occasionally strange "copies" of it are left lying around if one tries
  to drag it to the pinned icon locations).

  This may be because quassel is a Qt based application, but I also run
  KeepassXC (another Qt application) without such issues (other than
  unusual window borders and icons which appear on both applications),
  hence why I'm unsure this is an issue in quassel or in the gnome dock.
  I'll attach a screenshot demonstrating the issue.

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