If clear commands are being run continuously on a clock, it causes problems with inventory management and crafting. It appears to cause a client-server desynch of the inventory, perhaps. While dragging items between spots in your inventory or the crafting grid and putting them down, occasionally they seem to disappear, even if it is not an item being targeted by the clear command. However this disappearance is purely cosmetic, as when you click again on the apparently empty space, you pick up the item(s) that had seemed to vanish. If this happens in the crafting grid, sometimes you see an item appear in the output that should not be there, but it fixes itself if you try to pick it up, or you'll pick up what it should have crafted. The effect is more noticeable if the clock running the commands is faster.

Banning certain items can significantly change the gameplay in fun and interesting ways, and this is the only vanilla solution to that. However this bug can make the game difficult to play, when it gets bad.