I made a command block with the command "/clear @a iron_sword 0 1" and attached it to a clock. Then I craft an iron sword. When I click on the sword, in the crafting GUI, the clock would pulse, without clearing the item. When the sword is later put in my inventory, it doesn't get cleared.

Afterwards, a few things may happen:
The command block randomly clears the item without giving an output.
The command block randomly clears the item and gives an output.
The command block doesn't clear the item but gives an output.
Also, if the item is clicked on in the inventory, the same things can happen.

Steps to reproduce
1. Create a command block that clears a crafted item(ex. torch).
2. Attach a clock to the command block.
3. Put a comparator next to the command block and add something to record outputs
4. Craft item(torch), without shift clicking the item to instantly put it in your inventory.
5. Watch the comparator output unpredictably.