I don't know if anything can be done about it or not, but it's happened the last two times my character has been bleeding on the ground and then recovered their pack. It seems that faction items; such as the watch key and rod, seem to be eaten whenever this happens. More annoying than anything else, so anything you can do to prevent it would be great.
Bag Bug
If you put them in boxes and they are fully packed, item loss is common.
If items aren't the same size, their order gets switched around when you pick up the container again, and sometimes things don't fit and get destroyed. You need to either leave things only partially filled, or make sure every item is the same "size" (only potions and misc. thin in one box, only notes, maps, and helmets in another, etc.)
Putting the most important items in the container first usually helps make sure less important things disappear instead, too.
Yeah, what they said.