Same thing just happened to me multiple times. Makes no sense. How do you go to war for your freedom, LOSE, yet still get your freedom? You can win a war and still end up losing. Seems like vassals have a time limit then, wish the game would actually tell you it. You can tell this game is new because of silly stuff like this.

I just ran into this bug today, so not at fixed as they think... Vassal demanded freedom, I refused, stomped his ass, forced him to surrender and now need to pay 145 warscore to make vassal again?

I know that it worked at some point as intended. The repayment is not intended.

I have run in the same situation, the point is that it will cost you 0 points only if there is the liberation demand. So if you refuse it, than you will have to vassalize them again

So, find out potentially there is such exploit: 

you force your liege to an ultimatum, he refuses it, you declare war on him, and get freedom if he haven’t enough points. So need to bug report this issue