Using the /clear command in any way clears any item out of a players 2x2 crafting-grid.

 

It does not matter which selector you use (as long as it is a player, of course), wich item you clear, or what amount.

Example:

1. (Create &) Open any world between 20w07a and 20w19a (newest snapshot at this time)
2. Use either a datapack or an active repeating commandblock to run this command every tick: /clear @a dirt 0 or /clear @p stone 1 (or any other varitation, as I said)
3. Try to put any item(s) in your 2x2 crafting-grid in your survival inventory.
4. The item(s) is/are gone.

 

The bug is since snapshot 20w07a, in 20w06a it wasn't there.