[1.12.2] What could cause individual items to disappear from a JEI recipe?

I've seen mods disable recipes entirely, but never remove individual items. I'm just mashing a couple modpacks together, so I want to know what could cause this specifically so I can tweak from there. I've only seen this on the vanilla stone tools so far. I've looked through crafttweaker and tinker's construct configs but couldn't find anything.