The above stack trace seems to be tied to this other message:

Nov 16 11:41:38 scruffy gnome-shell[5626]: Object Meta.WindowActor
(0x560d5092bb00), has been already deallocated — impossible to access
it. This might be caused by the object having been destroyed from C code
using something such as destroy(), dispose(), or remove() vfuncs.

The error seems to be on the disconnect() call in
Transparency.disable():

        for (let key of this._trackedWindows.keys())
            this._trackedWindows.get(key).forEach(id => {
                key.disconnect(id);
            });
        this._trackedWindows.clear();

Presumably the remainder of the clean-up performed by this function and
its callers is not performed, leaving the shell in an inconsistent
state.

I'm still not sure why gnome-shell is trying to disable the extension.
Does it disable extensions when locking the screen?

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https://bugs.launchpad.net/bugs/1769383

Title:
  Ubuntu dock/launcher is shown on the lock screen

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