I removed all but Desktop Icons, Ubuntu AppIndicators and Ubuntu Dock, rebooted and then reproduced the issue. Luckily I’ve found one way to reproduce this, albeit somewhat convoluted and still a bit unreliable, involving Synaptic and window tiling. And as it doesn’t seem to trigger the issue when using another account, I’m now working through settings differences between the two in hopes of finding something crucial.

While doing so, I did discover that dconf-editor is similarly affected:

    touko 12 16:09:32 saegusa gnome-shell[8208]: WL: compositor bug: The compositor tried to use an object from one client in a 'wl_pointer.enter' for a different client.
    touko 12 16:09:32 saegusa gnome-shell[8208]: WL: error in client communication (pid 12364)
    touko 12 16:09:32 saegusa dconf-editor[12364]: Error reading events from display: Katkennut putki
    touko 12 16:09:32 saegusa boinc[2098]: No protocol specified
    touko 12 16:09:32 saegusa boinc[2098]: No protocol specified
    touko 12 16:09:33 saegusa boinc[2098]: No protocol specified
    touko 12 16:09:33 saegusa boinc[2098]: No protocol specified
    touko 12 16:09:34 saegusa gnome-shell[8208]: WL: compositor bug: The compositor tried to use an object from one client in a 'wl_pointer.enter' for a different client.
    touko 12 16:09:34 saegusa boinc[2098]: No protocol specified
    touko 12 16:09:34 saegusa boinc[2098]: No protocol specified
    touko 12 16:09:34 saegusa gnome-shell[8208]: WL: error in client communication (pid 12796)
    touko 12 16:09:34 saegusa gnome-terminal-[12796]: Error reading events from display: Katkennut putki
    touko 12 16:09:34 saegusa systemd[3569]: gnome-terminal-server.service: Main process exited, code=exited, status=1/FAILURE
    touko 12 16:09:34 saegusa systemd[3569]: gnome-terminal-server.service: Failed with result 'exit-code'.
    touko 12 16:09:34 saegusa systemd[3569]: vte-spawn-da1941e8-60e5-48e5-868b-7348dd1158c7.scope: Succeeded.
    touko 12 16:09:34 saegusa gnome-shell[8208]: Error adding children to desktop: this.layout.get_child_at(...) is null
    touko 12 16:09:34 saegusa gnome-shell[8208]: Error adding children to desktop: this.layout.get_child_at(...) is null
    touko 12 16:09:34 saegusa gnome-shell[8208]: Error adding children to desktop: this.layout.get_child_at(...) is null
    touko 12 16:09:34 saegusa gnome-shell[8208]: Error adding children to desktop: this.layout.get_child_at(...) is null

Looks like dconf-editor did not exit with FAILURE, but the dconf-editor window did disappear just as Gnome terminal’s did.