I’ve only tested this with plastic bottles so far as my character can’t really get into the rest of the city yet, but whenever I fill bottles with water or try unloading water from a bottle, the stack will randomly change the amount of water. For instance, I brought 6 plastic bottles to a house and filled them from the bathtub. At first, going into inventory showed there being 6 full bottles of water. When I dropped one of the bottles, the other 5 emptied. When I picked up the one I dropped, they filled again.
I took the water back to camp, confused, but wanting to boil it. Trying to unload a bottle to hold clean water resulted in half of them emptying, and not on the ground unless it no longer leaves a water symbol where you unload on the ground.