The cover must mostly rest on the water surface or it can (usually will) pull the track off of the coping. Given the fluctuations in water level of a spa, I'm not sure you could get them to make one any smaller for warranty liability reasons. You'd have to convince the dealer to send in false measurements, which is unlikely without a waiver for the same liability reasons. Nobody wants to buy you a new cover and fix your coping for free because you don't like wrinkles.
Lower your water level an inch or 2, see if it goes away. If not, call the dealer, those things can slip anchors on the shaft and go loose in one spot.