If you’re doing something akin to milling, scouring, prospecting, etc, then after the first create it will default to using the first stack in the ui. The materials show up in the ui in the order that they are in your bags - left to right top to bottom, with backpack first, then bag 1,2,3,4, reagent bag, and then finally the bank. Reorder the materials to keep that first stack topped off to avoid these crafts failing.
Basically, even though I have selected the blue stack to craft from, only this stack in red matters after the first craft.
I’ve only had it do this when manually selecting material ranks. Using the default lowest quality (use highest quality unchecked), it will automatically start consuming better materials as lower ones run out.