When using helmod to calculate "coal crushing" which is added by the mod "Crushing Industry", it does not correctly output the products. The recipe has coal in both the input and output (i.e. 1 coal --> 1-2 crushed coal + 5% coal + 2% stone), and when selecting the recipe without productivity Helmod correctly calculates it. However, when you add productivity via prod mods, it seems to decrease the stone and coal output into the negatives.
Interestingly, this issue only seems to affect recipes from "Crushing Industry". Recipes from other mods where it has a chance of returning the input are not affected (e.g. "gold crushing" from "Lignumis")