Just started up a new world, and tried to merge two of my swords to save inventory. The two sowrds got left in the crafting area, but got the repaired sword as well.
i tried it later with picks, and diamond swords in a creative world, same result.
rejoining the game lets me keep the dupes.
Duplicate of MC-46715 - If you have not, please use the search function in the future, to see if your bug has already been submitted. If you could not find the original report, please comment with the keywords you searched for.