I have a problem that I suspect might be caused by the same underlying bug:
I have a self-compiled (don't ask) Firefox Developer Edition in my dock as a persistent app, and every once in a while the dock gets the idea that the copy of Firefox that I have open is not the copy I have stored in the dock and adds a second Firefox icon in the non-persistent apps section. Whenever this happens, the touch bar dock widget shows the normal copy of Firefox as a blank space with the running dot and tapping it does nothing.
Sooo... probably the same bug in BTT, but triggered by the dock getting confused rather than by opening two copies of the same app.