Whenever an item disappears from a player's inventory (by dropping it, moving it around, etc.) while his/her inventory is opened, and another is given back immediately, it does not show up.
Here is a detailed investigation of the bug (sorry if I am not articulating very well in this video):
https://youtu.be/XT0mcDEECE4

What I expected to happen was...:
When an item disappears from a player's inventory and one is given back like described above, the given back item is visible in the player's inventory like it should.

What actually happened was...:
The given back item is not visible, but still there.

Steps to Reproduce:
1. Get three command blocks (/give @p minecraft:command_block)
2. Place the three command blocks in a chain, where the first command block is a repeating command block and the other two are chain command blocks. They are all set to 'Always Active' or powered by redstone.
3. Paste these three commands into the command block in this order:

/scoreboard players tag @a[tag=HasStone] remove HasStone
/scoreboard players tag @a add HasStone {Inventory:[{id:"minecraft:stone"}]}
/give @a[tag=!HasStone] minecraft:stone

You have now succesfully set up the machine. One piece of stone should be placed into your inventory now.
4. Drop the stone from your hotbar.
5. Notice that one is given back by the machine.
6. Open your inventory, and drop it immediately form there by hovering over the item and pressing 'Q' (by default).
7. Notice that it looked like you got another piece of stone back, but you can't see it in your inventory.
8. Get a different block and place it at the spot where the item should be (usually the first or the second slot in your hotbar).
9. Notice that the stone now shows up.
10. Repeat step 4 and notice that you get the item back again.
11. Move the item in your inventory.
12. Notice that it looked like you got another piece of stone back, but you can't see it in your inventory.
13. Close your inventory and type this command in your chat:

/scoreboard players tag @p list

14. Notice that you do have the tag HasStone, but you cannot see stone in your inventory.
15. Repeat step 8 and notice that the stone now shows up.