The auto crafter has a couple of problems.

First of all, it eats buckets and similar items that have a remaining item when crafted.
Secondly, its inventory only doesn't accept two stacks of the same item. This is actually a pretty cool feature, but this means that crafting recipes that use more than one unstackable items are impossible. Cakes for example.

*Fixed container items being lost by the autocrafter- they now get put into the input slots
*Instead of the autocrafter only accepting 1 stack of each item type, it now accepts 1 stack PER ITEM USED IN THE RECIPE; For example, the stone pickaxe recipe now allows 3 stacks cobble and 2 stacks sticks into the input slots
*Automation (hoppers, pipes, etc) can now remove any item from the input slots that aren't allowed to be there (AKA, buckets that were put in there when crafting cakes)

Fixed in 2.6.4, available here: https://www.curseforge.com/minecraft/mc-mods/essentials/files/2836391