I've had this bug occasionally ever since the original release of the game - it isn't new with the new patch. I've seen it both with conquered puppets and gifted (spoils of war) puppets. I've noticed in these cities that if I annex them, they'll typically have a unit in their queue already started. It's been awhile, but I believe that fully exiting the game and reloading, and advancing a turn has fixed this for me in the past.
EDIT: I should read more closely. I assumed this was talking about the nothing-in-the-queue bug. Apologies for erroneous info.