Vassals stay in faction no matter what.

[Rad7For]

Hey, some of my vassal stay in faction even though their opinion is +100 is that a bug?

[Taiwan Number One]

I think it is as they are supposed to drop out if they have 75 or higher opinion of you.

[Arkeangel]

It happens sometimes, I've had vassals with 100 opinion join independence factions.

[markdb92]

Throw your vassels in jail and rot there. They auto leave faction that way.

[Nef]

I'm not sure it is a bug, I think it has something to do with how powerful said vassal is. I've only really noticed it with my most powerful vassals. For example, in my Britannia game, the king of Andalusia ammassed a huge amount of power, and he and his descendants were almost permanently in the Independence faction.

Think about it this way... your character's opinion of your liege doesn't really affect your decisions as a player (unless you're REALLY into roleplaying!). Even if you think your liege is the most awesome guy ever, you might still want a chance to strike out on your own!

[Thundercomet]

Vassals can also scheme to get other vassals into their faction for a while through blackmail or something like that.
Possible that's going on here.

[Red Shift]

Do you have vassalage over any of their de jure holdings? Even if its just a city or some such, they will see faction as the only way to get what is legally theirs, regardless of opinion.

[La Follet]

also kingdoms will join the independence faction if their kingdom is not a de jure part of the empire.