Regarding late fee

As per my thinking, if you filed last GSTR 3b(September, 2018) late , than late fee of that return is auto reflected in current month GSTR 3b.(kindly check this in your case that, is that penalty is related to last return late filed?)

As in current month GSTR 3b late fee reflected is relating to last month's late filing, which was not waived at that time.

So, you have to pay that late fee, and from next month it will be charged as per Notification. 57/2020 i.e. ..Nil or restricted to 500/-.