You could hunt for books and increase your skill to/past the requirement for the recipe. I know that’s still not much of a solution, and essentially the only alternative to limiting your cooking choices to recipes you are guaranteed to succeed at…
You could always mash your face against the keyboard until the trauma causes you to forget that you still have to confirm a few bajillion more times in order to boil water at level 0.
Regardless, I’m glad that I’m not the only one experiencing this. Though, I think the problem is not the persistence of the messages, but the fact that none of the materials actually get wasted. My guess is that the implementation is incomplete for wasted liquids in crafting, ever since crafting got a bit of an overhaul. I don’t really know though.