Some large scale rebellions are handled by events, under some conditions, that I can not indicate because I'm not the one handling historical events. But you can also get minor to major rebellions from the code itself, based on the loyalty of your regions, who is populating them, and what is the relationship the population (the faction having control over them) with the occupying nation. To be more precise, there are no less than 4 types of revolts:
a) social uprising, if you are not satisfying enough your population (they can not buy food or luxuries in quantity, or militancy is too high). This can lead to strikes or even uprising.
b) Native revolts, in colonial regions, if you are too harsh in your colonialist approach. Some native are much stronger than others and are already made intro tribal nations before you arrive.
c) nationalist/irredentist revolts: a subjugated ethnic or nation want to liberate his soil.
d) partisans creations: the only one that can actually help you, if your country is being invaded. This is custom to each nation.
You can suppress revolts, but generally, if you don't operate at the root, they come back
