I have a similar issue. I think your on to something. For me, I recruited an army but didn't wait for them to join. Sieged a castle and immediately made peace. I can see that one of my companions that I recruited to my army is directly next to me on the map. The manage army screen shows the companion is in my army, but they are not. Game freezes as soon as the companion joins my army. Disbanding the army makes the companion move to where they would be if they were in my army, without me unpausing or starting time.