I am playing on a modpack with one 5x5 recipies outputting 2 items. Manually inputting the items in an advanced crafting grid allows me to correctly take the 2 items out of the output slot. However when attempting to autocraft them using Automation Interfaces, they only out 1 item. I suspect this is due to the item not normally being able to stack with one another. The item in question is Mekanism's Quantum Entengloporter.

I must say it's very interesting that I didn't get a bug report for this back when I was still maintaining the 1.12 version. Unfortunately I am no longer maintaining the 1.12 version so this will have to be considered a feature.