SARS REJECTING SO CALLED LATE DISPUTES

In Nov 2016 my son submitted 2016 return. Received verification letter on 04/11/16 to submit documents. Reviewed ITA34 came back for payment as EMP501 was not submitted by employer. Phoned on 7th SARS (unfortunately made no note of CaseNo) but was told to pay first and then lodge dispute with proof of submission by employer. Which he promptly did. After many calls to employer and being send from bookkeeper to auditor, he got proof of submission in April 2017. He then lodged DISP01 with SARS but they declined this as "too late". He lodged another DISP01 in which he explained that he could not have lodged this earlier as no proof by the employer could be supp**** to him. He lodged Notice of Objection and Complaint. Also rejected by SARS. The short of this is that he have paid PAYE twice in 2016 and has not been refunded or credited in 2017 for above reason. Was SARS not suppose to grant him a credit in 2017 (without him doing anything) for the over payment or double payment of PAYE in 2016 when the employer submitted their EMP501? And isn't it so that debt to SARS is not waived. So why is this not also valid from the taxpayer to SARS? I would love to hear from some tax experts on this.