Thanks to the many people who reported this to me. I didn't account for a second dupe bug which can be replicated in the following steps:

1. Place items in a crafting table
2. Go far away to unload the chunks that the table is in
3. Restart server (with /stop or /reload)
4. Go back to the table
5. Break table/remove items
6. The items will still appear there

It is urgent that you update! In order to delete the old floating items, you can use the kill command while standing close to them
For 1.8-1.10:
For 1.11+: