I've reported this aswell and it's very annoying. Only thing you can do is turn off unification but I'd prefer this to get fixed.
My unification is turned off, It does not happen in my inventory but mostly due to machine process.
Also, someone please tell me, how do I turn off requirement of plates etc. for tool and armor crafting? I just want to use ingots to craft pickaxii and armii, pl0x.
If possible. Please and thank you, kind sirs.
B:TooEasyMode=true does that I think.