Minecraft Version: 1.12.2
Smart Backpacks Version: 1.0.6

I was attempting to set up autocrafting using the infinite water upgrade and the crafting upgrade to speed up the crafting of mud (animania). When I put the materials in the backpack, the crafting upgrade used the bucket of water and the dirt to create mud, but didn't give the empty buckets back. Normally when mud is created, the empty bucket remains in the crafting inventory.

This happens with anything that doesn't consume all materials in a crafting recipe - i.e. the infusion crystals from mystical agriculture.