Side skirt on the passenger side isn't on all the way...I can see a gap in it and see the little white plastic pieces that bolt on to keep it on...the drivers side is perfectly mesh, so I know the passenger side one is off....

If I take this in should it be covered under the factory warranty??

That may fall under the 12 month/12,000 mile adjustment warranty. Then again your dealer may cover it. Never hurts to ask.