Has been reported before; https://forum.eclipse-rp.net/topic/84105-empty-water-bottles-refill-goes-above-the-inventory-limit/
Pretty sure devs/staff are aware of it, and hopefully they're just leaving it be until they can add a hotfix and/or replacement for refilling water bottles as it completely destroys cooking drugs in private labs primarily.
Personally, I don't think this bug should be fixed for now until there's a replacement but I had to report it as bugs are meant to be reported.
However, for a replacement, they should add a sink in furniture store that supports refilling water bottles through a WIM and costs like $50,000 to buy (could be more, since it'll be up forever and available for everyone) where when you refill water bottles, there's a 0.5s for each bottle being refilled making it 25 seconds to refill 50 water bottles.