update: I called the IRS and SSA. IRS does ping the SSA database to check on the SSN. That process wasn't clear to the lady I was talking but that was her understanding so she suggested calling the SSA which I did. They said my son's SSN is live and valid but it can take up to 30 days for that information to propagate to all databases hence that might be the problem.
I am going to file an extension and refile in 30 days.
