If you put two unbroken, unenchanted items in an anvil and name them, it takes away one item. I noticed this while experimenting earlier. Maybe block the ability to do this, as someone may come along and get rid of one of their diamond swords or something, just attempting to name them.
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I believe this is Working as Intended. The item in the right slot is always consumed. It is up to the player to figure out the most efficient way to use the anvil. Sometimes the experience level costs will vary just by switching the items in the two slots, and Mojang has said that this is intended. See MC-3880 and MC-4129.
Duplicate of MC-4665.
Did you put a stack of two items in the left slot for renaming or did you put one item in the left slot and another item in the right slot ?
If in the left slot, it it rename the entire stack, if the items are in the left and right slot, it will always combine/repair the items, regardless if you rename them too.