Thanks for the images! They helped narrow down the problem to angels refining, but I couldn't figure out exactly Why it was happening. The only recipe named after crushed stone ("stone-crushed" internally) is the hand-crafting of stone -> 2 crushed stone. My mod should simply invert the recipe as 2 crushed stone -> stone, but instead we get crushed stone -> 2 crushed stone. Maybe the logic is broken somewhere in handling "stone-crushed" vs "stone" or something else is weird, but it's difficult to test.
I did fix the issue though as of 4.0.10, although a little bit lazily. I just manually added a check for crushed stone to the logic =P
Next time you load up, the game should mention that recipe has been removed.