This issue is related to the ModTweaker support you added. Here is what I mean by the title:
I have this recipe here:

When I have 1 Terracotta and try to click the Cauldron, nothing happens:

When I have 2, I get 2 stained Terracotta, but only 1 Terracotta is used:

It is intentional that if you set a requirement of 2, you must have 2 items for the recipe to work. It seems that it is not properly consuming both items though, so I must have not fully implemented that behavior for the dye recipes.

Yeah, that's pretty much what I said.

Fixed in 0.1.4