The Gen1 had the same issues with paint coverage on the bottom of the doors! Mine did. They should fix it under warranty, if they give you a tough time about it ask for the customer service phone number and that should help.
Service manager submitted pictures to ford and they have approved the repair. I haven't had a chance to go back to the dealer to figure out what their game plan is for the repair. I just can't imagine how it made it through the entire assembly process and not one person caught or noted the paint missing.