Lets say I have a bag of flour and four little piles (0.5kg) of flour in my inventory (and a bucket of water), I go to the baking table and click craft all, As I use up the little piles I end up with two piles of 0.30 and 0.05 AND the bag of flour being marked as required. If I remove the bag of flour (to my backpack) and click craft I get the error "You do not have all the ingredients." If I close the craft pie dough window and open it again then it will work, because I do have enough flour.

Not knowing the code I can't say exactly what is going on but I can see where the problem comes from and imagine it shouldn't be too hard to fix. Like I say, it is trivial but it has cropped up a few times and it can be annoying/confusing, especially to new players.