When a faction is defeated its remaining armies/territory normally become rebels. However, I've encountered a glitch where an army which is in the process of occupying an enemy province when the capital falls will retain its affiliation to the defeated faction. This means that anyone who wishes to invade the province with said army must first declare war on the defeated faction (I haven't tried a faction that doesn't follow the Code of War yet). However, declaring war doesn't work because the game keeps giving you the message "you can't break the Code of War, you have to wait until next turn" regardless of how many turns pass. Such provinces also have a resistance counter that never diminishes. It ends up being an effectively inaccessible province that nobody can annex.