After going to war with empire that have vassal(s) and occupying cities of both, the peace deal is resolved correctly and occupation of enemy empire is lifted, however the occupation of the vassal empire cities persists. Below is save file attached. The save file is from end-game, however the war itself took part few eras earlier. The game itself is also from beginning of May, but I have been able to reproduce this bug recently (unfortunately forgot to save the game file).

VassalOccupationBug.7z