17.18 gstr 3b vs gstr1 clerical errors

In FY 2017-18, one month's GSTR3B was erroneously filed as NIL, though GSTR1 was filed correctly. The error was discovered only at the time of filing GSTR 9/9C and the same was reported. However, the window for making corrections in subsequent months for FY 2017-18 had elapsed by then. Now the client has received notice for making the payment of tax liability, without allowing ITC for that month. The books as well as GSTR2A rightly shown all the purchases. Only due to human / clerical error GSTR3B was wrongly filed as NIL. Can someone guide on this what can be done? Any good case law under GST or Service Tax or Excise which will be in favour of the assessee in such situations?