This sounds more serious than some friends of mine who have the dents, but they finally figured out that when they were putting their foot on the rear tire(s) to hoist themselves up (to stand on the tires to reach supplies in the box) their knees were putting small dents in the quarter panel above the wheel well. The skins on these newer trucks are thinner than ever.
Sorry, missed the inside out tag line. The above will surely strike a chord with someone who is wondering where the mystery dents are coming from.