Just to be sure what is happening, could you explain exactly what is happening with your liquid containers? I can't tell if you are saying that they passively lose liquid overtime, or if they spontaneously acquire new liquid. Any liquid container outside a pack with automatically siphon liquids from the outside area. Sometimes they still siphon when inside a handheld pack like a toolbox(?), but it's an inconsistent and infrequent bug, and I don't know what causes it
I haven't tested it, so speaking from my impressions. Liquids containers are not leaking. But all liquids containers that both have something in them and have free space can passively take in liquids from outside if you are submerged deeply enough. I don't know what counts as "deep enough" but it feels overtuned against you, just like many other things in this game.
I don't think it matters where a liquids container is on you - hands, bag, or a worn backpack. Or maybe it does and the bag must physically get submerged, I don't know.
Empty containers you have will never get anything in them from outside, unless you actually drop said container into the liquid, or pour a bit of some liquid into it first. Which suggests that there IS a bottle cap mechanic, but you don't have access to controlling it, it just auto-activates with an empty bottle.
The only container that doesn't seem to take in outside liquids is the one you can wear in the same slot as a fanny pack.
Submersion is when the wet moodle increases. So you can test when your Expie is submerged by slowly walking into water until it starts to rise.
The only thing I can think of to solve your problem is to delete your game files and reinstall to see if there is a packet loss problem causing liquids to ignore backpack containers
I still don't understand what bug you are talking about, Liquid containers taking on outside liquids when submerged is clearly intended behavior. I'm not talking about that, I'm being baffled why it's a mechanic in the first place, because it works off an insane assumption that you are putting uncapped bottles into your bags.
I was hoping the developer would read this and either disable the mechanic for now, or add a way to close bottles.