Quote from acap41
"Here are the steps I use to reproduce it. It's not the only way, but it's the one I used to test it when my players reported a dupe: 1) Acquire two sticks and three ingots, for an iron pickaxe 2) In a crafting table arrange the items as if you were to craft the pickaxe 3) Right click on the middle ingot and place it back in your inventory 4) Shift click the now-empty output slot 5) Collect duped ingots and sticks.

Sorry for being so vague about it, I just assumed you had already known about this since in the previous versions shift-clicking the output was disabled. I'll re-install this on my test server and see if I can get a vid of it."

Just released a test version here: https://github.com/haveric/StackableItems/blob/master/downloads/dev/StackableItems.jar?raw=true
which should fix your dupe problems. Let me know if you can still replicate the bug in any way or if this fixes everything.