Tax Liability regarding Contract with Central Government.

My clients having GSTIN. Now he is engage by cab service to Central Government with contract. Now my client not issue his tax invoice, but Govt. has made invoice on behalf my client. Now, his all GSTR-3B & GSTR-1 returns are filed was NIL. But, Govt. has deduct 2% TDS and same he has been filed TDS & TCS return and refund claim through CASH LEDGER. Now SGST department issue show cause notice for why should filed nil return ? 

As per attached copy of invoice made by Central Government.