i've narrowed the problem down to eating food from the ground through the VICINITY window and right-click 'Eat/Drink'

1. locate food on ground (quickest with 1 charge items like pop or fruit since cans require you to open them, have them show up in your bag, THEN drop it on the floor to eat it to reproduce this bug)
2. right-click the food through the VICINITY window
3. left-click 'Eat/Drink'
4. after consuming the item completely it will go away from your hands but a slot will be taken up in whatever container/slot the item would have gone to if you had put it in your container and eat it through there

so what appears to happen is the game doesn't have a way to dump the item when not handled through a container and dumps an empty food in your container upon finishing
this doesn't work with canteens/bottles as they can get refilled and pop back in your bag when you take them out of your hands (assuming you have the space)