If you attempt to clear an item directly after crafting it, it will become a ghost item that drops upon closing the GUI.
To recreate the bug
Add a recipe
Add an advancement to detect when the recipe is unlocked. Give that advancement a rewarding function that clears the crafted item.
Close the GUI.
Sample datapack provided in attachments ( Recipe is 1 dirt )
Attachments
Comments 2
This might relate to MC-147499
Confirmed using reporters datapack.
Could not reproduce on 1.16.4.