Ghost Pikmin

Ok, so many of us may already have found this wierd glitch where either you can't throw a pikmin, or pluck anymore. this is because the game thinks that you have pikmin, but you really don't, so you'll end up throwing nothing, or can't pluck anymore. what i want to know is, how is it caused, and how do we avoid it, this could become a bigger issue later on.

No one has publicly announced the reason as to why it occurs, but the whistle (Down+B) supposedly fixes the glitch.