I have a similar same issue on occasion. When I deplete a pick while mining, and then release the mouse button and open my inventory to fetch another pick (inventory tweaks will not refill enchanted picks, for example, especially when they have slightly different enchants due to the random nature of enchanting), there will suddenly be a copy of the destroyed item in the slot I try to place the new one in. The copy item has a completely empty durability bar and is only good for 2-5 uses, then it breaks again. And, of course, there might be another ghost copy appearing, just like after the first breaking. Sometimes it doesn't happen at all; other times I can have the same tool reappear on me 5-6 times in a row until it finally stays dead.
I've had this issue back on 1.2.5 on a Tekkit server as well, and potentially (though I cannot really recall properly) in singleplayer worlds as well.
Usually I just shrug and try to get rid of the copy item quickly. But since it has near-zero durability it doesn't matter much.