Sometimes the /clear command is glitchy and items remain in the inventory even after it's run and don't disappear until you update the item.

How to Replicate:
1. Make a new world (super flat, redstone ready, for testing purposes) in creative mode with cheats enabled
2. Teleport to 0,56,0 (For testing purposes)
3. Make a fast redstone clock (comparator clock for testing)
4.Attatch it to a command block with this command: /clear @p[x=0,y=56,z=0,r=0]
5. Go to 0,56,0.
6. Drag an item from the creative menu into your inventory.
7. Walk out of the clear zone. The item should still be in your inventory.