When you use an item and be given an identical item on the same tick that goes into the same slot as the item that was just used, a glitch occurs where the given item appears to not be in your inventory. When the item is in this "ghost" state, the item cannot be used. If you drop the item or in the inventory, click on the slot the item is in, the item will reappear on the ground or on your cursor respectively and work normally. The inventory fills up just fine and it does see the "ghost" item even though it looks like it isn't there. Other than that, item usage works as intended. This glitch works on any item that is completely consumed upon use like ender pearls, snowballs, most food items and more (other than tools and weapons that are broken on use)

Video showing the glitch in action: https://youtu.be/U3FsxzGPp8E

How to reproduce this glitch:

1. Make sure you are in creative mode and cheats are enabled.

2. Give yourself a command block and place two of them down that are chained together.

3. Set the first command block in the chain to repeating and the second command block to chained, both on always active

4. Type the following command in chat

/scoreboard objectives add EnderPearlsUsed minecraft.used:minecraft.ender_pearl

5. In the repeating command block, insert this command.

/execute as @a[scores={EnderPearlsUsed=1..}] run give @s minecraft:ender_pearl 1

6. In the chained command block, insert this command.

/scoreboard players set @a EnderPearlsUsed 0

7. Give yourself ONE ender pearl (this will not work with more than one ender pearl)

8. IMPORTANT: Set your gamemode to survival or adventure.

9. Throw the ender pearl. The glitch should occur.