How to reproduce the glitch:
1.Get a stack of empty maps.
2.Set command block with following command on allways active, and repeating:"/clear @a filled_map"
3.Spam maps
4.Now you can see that all filled maps get cleared except of 1. This one map that doesnt get cleared is ghost item meaning it get cleared when you put another item in same slot. You can also throw it out of inventory but when you pick it up it dissapears.
5. Fix the bug