Is it a true GT500 spoiler or the 3D Carbon brand spoiler that American Muscle sells? An easy way to tell is if the Gurney flap is a separate piece (real GT500 spoiler) or molded into the spoiler (like the 3D Carbon spoiler). If it turns out it is the 3D Carbon spoiler, the chances are the bolts were left out because they didn't exactly line up perfectly. I've experienced and know of a couple of other Mustang owners that have too. I had to widen the holes a touch on my deck-lid because of this. They looked right but were barely off (maybe just the angle was off and caused interference).
I really like the (knock-off) GT500 spoiler on my car!