Continuous crafting works fantastically unless you're crafting honey out of honey bottles. After shift clicking the output item once, it leaves a single empty bottle in each of the four input slots and doesn't refill it with honey bottles

This looks like more of a minecraft bug. Shift+Click on the result slot doesn't clean the matrix for some reason and always leaves 4 empty bottles.

I'll look if I can do something about it, but the implementation of auto crafting is fairly complex already. So either it will take some time or won't be possible at all.

fixed in e771347