Did the IRS cash the check, i.e. did it show up as paid in your bank account? If so, then the IRS has the money. They just didn't credit it to your son's account, because of the wrong SSN. Your son has to call the IRS to straighten it out. If your son is too young to call himself, you should be able to make the call.
If they did not cash the check, stop payment on it and pay what the IRS notice says he owes.
