I’ve seen something similar involving equipment (weapons and armour) in the past, which may or may not be related to the same underlying issue. It was nothing to do with auto-loot, since I had it disabled. Also, the inventory wasn’t even close to full when I took the loot. But certain weapons and armour remained stuck in the inventory and couldn’t be assigned to any character. I think it was possible to repair and sell them, but not to make use of them. I thought I knew what had caused it, but I was unable to reproduce it in the same campaign or in a fresh one.