GSTR-3B Late Fees

For july 2017 to january 2020 returns late fees of rs. 500 per return will be chargeable , if filed before 30th september 2020

Since Central Tax payable is not nil, GSTN portal is asking for late fees which is however restricted to Rs. 250/- each

Even I don't have any nett liability of Central Tax

As per the proviso in the notification 52/2020 the waiver of late fees was there for if the total amount of tax payable is Nil for the returns pertaining to July 17 to Jan 2020 filed btw 1st July to Sep 30th 2020. in your case the net cash payable is not there. however liability was there which was set off against credit. therefore Late fees of Rs 500 is applicable

Try to file in time return