There seems to be an inventory bug with the Enhanced Edition that didn't exist in the original. Two things cause it to occur so far in my experience:
Sorting inventory by type
Removing a piece of armor and placing it on a different type of item in the inventory that can't be worn in its place.
The issue is consistent and repeatable. The items seem to be destroyed, but when you go into the sub-inventory categories, the item is still there. It just doesn't show on the main "all" items view anymore. Issue is persistent through save and reload.
I was able to recreate this bug as well. Very odd!