Dear Hardik,
As per Notification no. 19/2021 - CT, maximum late fee for filing returns for period July'17 to April'21 is Rs. 1,000/- (CGST & SGST of Rs. 500/- each) where the tax liability is not nil. Returns of such period (in your case Nov'21) should be filed in 01-06-2021 to 31-08-2021. Since the late fee auto filled is more than the capping, it depicts that the amnesty scheme is not reflected in portal yet. Following procedure could be followed to filed returns considering late fee could not be modified manually in portal -
1. To file a grievance in the portal.
2. To pay the late fee as per portal and file returns, as more delay would lead to more interest & late fee again.
3. To apply for refund of excess late fee paid along with attachments of correct computation of late fee, Notification no. 19/2021 - CT and grievance filed.