I'm sorry about the title, this is just a bit of an odd issue. I didn't have the inventory space to remove a recipe (The Chalice, I forgot it needed 5 relays and not 4), so I decided to move all the items for the old recipe to the very top row of the gui, place the needed recipe (The relay), and noticed that I could craft the relay. So I crafted it. And it succeeded! Except it also stole 1 of each item stack that was unneeded. To be honest, I'm not sure if the bug is it stealing the items, or the ability to craft a lower tier recipe in a higher tier altar when there are items in the non-lower tiered altar slots.

This is SP and I'm on the latest version of AS.