When trying to fill 2 plastic bottles with water from a pond or a fountain, the character will always take that bottle in hands you filled up first despite equipping the second one.

So if you drag & drop the second bottle (empty) in hands, the hand icon in the inventory will appear for the first one (already full).

However, if you take another item in hands (e.g. gun), then empty your hands you can take the second bottle and fill it up.

Not sure if it's the same with canteens.