The foal was not genetically black. It is simply not possible considering the mare’s agouti status. She CANNOT produce a black foal.
I have no idea how color develops in utero, though, and perhaps the foal would have appeared to be some version of bay or brown if it had been carried to term. Or perhaps the color would have developed in the first shed. But the foal would have been bay or brown if it had lived.
If you would like more information about what version of agouti your mare carries, you can send hair in to Pet DNA for their seal brown test. No one else tests for seal brown. That test will only elucidate if your mare is AA or carries At. Seal brown is the very dark–nearly black–version of “bay” with some lighter points at the muzzle, ears, flank and behind the elbow: http://en.wikipedia.org/wiki/Seal_brown_(horse)