A guy at my work has a 2012 ( i think) White King Ranch F-250 with the same problem . Says so far Ford is refusing to do anything . I asked him if the truck was ever repainted before . He said the front bumper was done . But he said the rust is all over the truck .
The reason why i asked him is because usually rust forms underneath the paint . Not the paint rusting . This leads me to believe that the rust impurities were somehow laid onto the paint from something . Someone above said rail yard dust . But not sure if that would happen . The paint on the truck would have been dried already from the factory .
Other causes would be painting in the factory then impurities in the air stuck to the truck while paint was drying . Possible but factory paint is usually very good .
Or being repainted at a body shop and they have a bad spray booth that allows impurities to be in the air and then it falls and sticks to the paint . Or them welding or working on a section of the car (welding or sanding) and they do not tape off the whole car . Then the flakes fall and stick to the paint and windows . Then they only paint the fixed/damaged area and do not realize the materials that landed on the rest of the car .
Brake dust . Semi metallic pads thowing dust up that is so hot it sticks to the paint . The most common thing about pads is when someone goes metal to metal on the pads and the wheel and fenders turn orange from the metal dust .
Just some ideas .