Regarding late fee

late we waved only upto sep. 2018 after that late fee is applicable

Yes... Late Fee applicable from October-18 return...

As per Notification No. 75/2018, CT and Notification No. 76/2018, CT , both dated 31-12-2018, seeks to fully waive off the late fees payable on account of delayed filing of Form GSTR-1 and Form GSTR-3B respectively for the period beginning from July 2017 to September 2018 and the Due Date to file the return and statements for the mentioned period is 31-03-2019.

Hence, late fees would be applicable on account of delayed filing of FORM GSTR-3B and GSTR-1 from October 2018 onwards.

Warm Regards.