Make sure you are not opening a duplicate.

• I have searched the issue tracker and did not find an issue describing my bug.

Description of your suggestion.

So to make croptopia's recipes you need to use the specific bottle by crafting it with a bucket. But when consumed it turns into a normal minecraft bottle leading to a huge stackup of normal glass bottles that i cant refill and use.

Id love a feature to just use normal water bottles or make some way to obtain the croptopia ones without ending up having to make more every single time i want to craft something.

I looked through the git history and I don't think the croptopia bottles that get crafted have ever returned an empty bottle. If you really want vanilla water bottles to work I'd recommend making a datapack and changing the waterbottles tag to include minecraft:potion
https://github.com/ExcessiveAmountsOfZombies/Croptopia/blob/master/shared/src/main/resources/dependants/platform/tags/items/water_bottles.json