I first suspected this when I saw no manpower with the vassals, even though their regiments hadn't been in combat. So when I had won the siege against a count and was ready to make peace, I checked the vassal armies, and there was one at sea, still on its way to the enemy province. I checked their home province, which had no regiment, since it was at sea and at full strength. Then I made peace, and on the next day the regiment at sea disbanded, and their homeprovince had only the accumulated manpower since mobilization.
Unfortunately I don't have a save, nor can I mail large files, but this seems to happen often and shouldn't be hard to reproduce.
Oh, and in case it makes a difference, this was while playing a game and updating to the next beta occasionally (not within the aforementioned war though)