Late fee for the month includes late fee charged due to delay in filing of GSTR-1, GSTR-4 (Taxpayers who have opted out from Composition and late fee was not paid fully in the GSTR-4 of that tax period) and previous month's late fee charged due to delay in filing of GSTR-3B. The computation is based on the formula: [Date of Filing – Due date of Filing] * ₹25/day (in case of any liability) or ₹10/day (in case of nil liability)] per Act (CGST/SGST). To view details of late fee click on 'Late Fees'.
Sir may be you have only paid the taxes. you have to pay the late fees also then u can file the return as per this message last month's 3B was also file after due date. hence this late fee.
The liability appearing in the below table may also include the liability that would have arisen on rectification/ revision of credit availed in original TRAN-1, if any along with the liability declared in separate tables of GSTR-3B. An intimation to this effect is already mailed to you on such revision/ rectification and the amount can be reconciled from the same.
Sir, late fees of march shall be auto populated in april months 3B. currently late fees which is showing must be because February return was filed late.