It appears the Ford assembly plant did wheels and brakes backwards from their sales brochures on the 2016s. From what I have been hearing and reading, the silver wheels are arriving with red calipers while the black wheels have unpainted calipers. Not sure what the resolution will be.
The gray wheels that became standard this year were an option in 2015. Part of that option pkg included red calipers. It appears Ford left the same code in the system that tells the assembly line what parts to install during a build. So, the gray wheel code calls for the red calipers and they get installed with the wheels, this time as standard equipment for 2016. They added a new code for the black wheels and didn't include the red calipers in the black wheel option. It's either laziness, or a simple oversight. Ford should have generated a new code for the standard gray wheels without the red calipers and either added the red calipers to the black wheel option, or, forgotten about them altogether.