The Auto Crafting Station, when used with Harvestcraft, moves the non-consumable (mortar and pestle, bakeware, mixing bowl, ect.) into the output and does not reuse the tool to continue crafting the recipe. A courier constantly assigned to moving the non-consumable back into the right place serves as a workaround, but is not ideal. Tested in Superflat. I suspect this is not unique to Harvestcraft, but have not tested with other mods.

Used:
Minecraft 1.12.2
Forge 1.12.2-14.23.3.2655
ancientwarfare-1.12.2-2.5.177
Pam's+HarvestCraft+1.12.2t
CodeChickenLib-1.12.2-3.1.6.339