This happens when you hold an item with your cursor, (not in main hand, not in inventory.)

For example I crafted a wooden axe from the crafting table and hold it with my cursor, then a command of "/clear ChichaST minecraft:wooden_axe -1 1" executed, the output showed that 1 item is successfully removed (and returned the result as success.)
However the axe was still on my cursor! I put it into inventory, it remained there after i close the GUI and check my inventory again.

One interesting thing is that, if you hold an item with cursor, run the command to clear it, then put it into inventory, and hold it up again, it disappeared! In other cases the item remains existing normally.

I was trying to build a system to ban certain items from crafting, so that if you craft the banned items, it will get removed and return the ingredients to you. With this issue the system is not going to be functional, I'm pretty sure this problem is caused by a bug in the /clear function, please fix that!