My son and daughter were also issued a German Birth certificate when they were born. It's automatic, they received their American Birth certificate from the American Consulate in Munich, Germany when my husband registered them when they were 6 weeks old. I could not register them with the American Consulate because I was still a German Citizen at the time.
Maybe you did not register your son with the American Consulate, which I assume was in Frankfurt, or perhaps Kaiserslautern?