Kristopher,
What you are describing is called "ghost shifting." And it '''is''' annoying. If you have the rear derailleur adjusted properly, perhaps you have a bent [http://youtu.be/jbSBQL08VHA|derailleur].
Or it may be that it is hung improperly and out of [http://www.ridemonkey.com/forums/f19/ghost-shifting-problem-need-advice-177723/|adjustment or incompatible] with your rear cassette.
Another cause is worn out parts, both the chain and the rear cassette.
Good luck with this repair.
Frank