I've noticed it myself, and in every case I've seen it's been a direct result of the new vassal rules.
There are two things that can cause this situation:
Situation A: Country A DoWs Country C, and brings Country B, its vassal into the war vs C.
Country B occupies Country C. Now Country B will not peace Country C due to the new vassal rules, and Country A will not either in the capacity of alliance leader since it wants more from the war. End result is a never ending war.
Situation B: Country B DoWs Country C. Country A is it's overlord and in the same alliance. Country B once again occupies C. Being alliance leader and vassal, it cannot peace. Country A will once again not peace either due to no warscore between it and C. End result again is a never ending war.
The same things can happen on defense that once again lead to never ending war. Add permutations such as the vassal occupying one province and the overlord occupying the other, and you still get situations in which neither country will peace and the war continues on forever.
The best solution is probably to rework the vassal rules to apply only to human overlords. I don't think human vassals should benefit from them either, as that has the potential to screw up wars in MP.