I think it was parked in the bay so that the paint job doesn't show. Go back immediately on Monday and explain this is unacceptable as you paid good money for a car and no damage was disclosed (was it during the buying process?) and you want the door properly repaired/reprinted.
that right there could've been the difference for the price and explain the low cost.
I just bought a car a couple of days ago and it's considerably less (3k) than similar from same year but it's due to a higher mileage in comparison to others. 2012 Civic SI sedan with 110k on the odometer. I was willing to go with higher mileage because I was able to get the car and warranty for two more years for less than 15k.
good luck with the dealer, they will state 'this is how it was when you bought it and never mentioned it during delivery'. ****** paint jobs typically show in natural light and are much easier to spot outside.