I'm just going to write this bug report in bullet-points:

1. Went to war with the Mongols. My grievances were about the two cities of their vassals, the Greeks.

2. I conquered all of the Greek cities.

3. Popup "Greece is no longer a vassal of the Mongols!" I'm still at war with the Mongols, Greece has 0 cities or troops, but they're a ghost civ trying to trade with me.

4. I ignore all of Greece's diplomatic attempts because I'm occupying all of their cities...

5. I defeat the Mongols and make THEM my vassal. They cede the Greek lands to me, but it doesn't count. It says I'm occupying Greek cities even though I'm not at war with Greece.

6. I have to declare a surprise war on Greece in order to settle the issue because it's impossible to generate grievances against them. They still had 0 Warscore, so they were willing to give me 2/3 of the cities or become my vassal the following turn. I'm called a "traitor" now, but it's okay.