You might have received complaint about late fee being applied in case of Sept month GSTR-3B. This is not for any delay on filing of Sept month as we have not reached 20th Oct. It is on account of late filing of return for previous period.
The system does entry into ledgers from 3B return on the date on which return is submitted (entries get frozen). The late fee till that date is applied, if date of submission is later than the last date of filing. In case the return is filed later than the date of filing then the late fee for the gap between date of filing and last date of filing return or date of submission (whichever is later) is added in the next month’s return.
In case a taxpayer had submitted last month’s return on 22nd Sept (D1) and filed the return on 26th Sept (D2), then late fee was calculated for 22nd -20th Sept and shown in the payment sheet of Sept Return (2*100*2). . The delay between date of submission (D1) and date of filing (D2) [26th -22nd Sept] amounting to 4*2*100 is to be paid by the taxpayer. The same is now being added in the return and shown to the taxpayer.
Hope this clarifies the position.
A ticker has been put on the portal explaining this. Please disseminate this to taxpayers