/clear does not work propely

When running /clear [Player Name, @p, @a, or @r] minecraft:[any block or item] through a Repeat Always Active command block will sometimes not clear the item, but instead will stay in the inventory as an invalid item. This item:
1. Cannot be cleared at all using /clear.
2. Cannot be placed (If it is a block)
3. Cannot be gotten rid of by pressing Q.
Sorry for no video about this, the video I created was more than 10MB.