I think your ability to imprison/revoke titles of the rebelling vassals is affected by whether you agreed to a white peace or the surrender of the rebels.
I recall that when I agreed to a white peace in one independence war, only the faction leader was imprisoned. Never again. When I next fought an independence war, I rejected their pathetic peace offers and beat them down to 100% warscore, and was able to imprison and revoke titles from every single one of the rebelling vassals except those whose original leader had died during the course of the independence war.
Also, did your ruler die during the course of the independence war? Not necessarily from death in battle, but for any reason. This seems to mess with the casus belli and what you're able to do to your vassals after you've imprisoned them. For example, I wanted to imprison a troublesome lord but failed, causing him to rebel. Before I could siege him down, my ruler died, and his successor was unable to revoke the title from the rebelling lord.
I think the threshold of positive relations needed with a vassal to dissuade them from joining rebellious factions needs to be much lower. Until they fix this, I will simply throw every troublesome and potentially troublesome vassal in jail regardless of relations, unless I need them to produce a heir to avoid getting inherited by another vassal. Or if their successor has the potential to be even more troublesome than they were.