When ever multiple Water bottles or other items that have refill properties are in your hot bar you can not select those items separately as they are stacked.
This has been most noticeable with water bottles. In order to refill a water bottle it must be in your hand. The easiest way to do so is to select it from your hot bar, then refill it. However if you have multiple bottles, they will stack, and the UI will not let you choose between them. So the only way to fill your second, or third bottle is to fill the first one, remove it from your hands, then drop it, then use the hotbar to grab the second bottle to fill.
This is a very cumbersome problem.