It could be a city rebelling without access to any rebel units
But if that was the case, wouldn't the game only CTD on the Rebels turn?
There are two cases, one where a city revolts to the rebels and one where it revolts to a faction.

When it revolts to the rebels it draws units from any that are buildable in that city first and if there aren't any it gets them from the list of units for random spawn rebel in that province.

When it revolts to an AI faction (or your faction) it does the same thing except if there are no units buildable in the city then the game pulls units from the local mercenary pool instead of the local rebel list.

In the second case at least, if there are zero units available (no unit buildings and an empty merc pool), then the city revolts with no problem. The city just has no garrison after the revolt. So I think the problem is, sometimes at least, some kind of incompatibility between either a merc unit being spawned for a revolt and the faction it is being spawned for.