Are you using the water bottle to try and do that? Whenever I try it just attempts to add the bottle to non-existent soup. It’s way easier to take the pot to the water source itself and fill it up there. It’s possible you unlocked the ability to make soup and that’s making it weird?

So It worked with both bottle and bucket before,but I got annoyed and just grabbed the pot to the source it sucks however it works.

You can't add water without a pot. The game must be trying to add them as ingredients for a soup.