Mine has the same issue on the rear driver's side and others have mentioned the same thing in other threads. The most cost effective route would probably be to sand it smooth and repaint it with krylon fusion spray paint (made for plastic/vinyl). So far I've just lived with mine since it's in the back and I don't see it often.
Common problem, a lot of us have the same peeling. Both of my 10 GT's rear doors are doing it. There is a thread about it on here. Someone had their door repainted by the dealer, but due to the texture on the door, you can't really sand it and repaint it like normal and have it look the same.
Thomas
the "Mustang Guy"
1987 5.0 LX Mustang
2016 Mustang GT - current daily
2004 Satellite Vibe &
2009 Red Vibe GT -twin's cars
2003 Neptune Vibe GT - prior daily
2010 Red Vibe GT - RIP 6/16/14
2006 Platinum Vibe - son's car