if you shift click craft something with more potential crafted items than the amount of liquid in the bucket (say, 11 XL Food Mod waffles with a diamond bucket thats 10/10 filled with milk), the recipe will consume the bucket as if its an extra use of milk or whatever liquid bucket and the bucket will disappear.

I'm going to close this as I am no longer maintaining the 1.12 version. I tested in 1.19 with Creosote from Immersive Engineering and it works as expected. There's always the potential that a mods custom recipe doesn't handle container items properly which could potentially be the cause of issues like this.

Thanks for the report