GST returns are routine work, which is exactly why they go wrong. Most of the notices we see are not the result of anything complicated. They come from small habits that repeat every month until the department picks them up.
Here are the five errors that account for most of the trouble we are asked to fix.
1. Treating GSTR-1 and GSTR-3B as separate exercises
GSTR-1 reports your outward supplies. GSTR-3B reports your summary and your payment. If the two do not agree, the mismatch sits on record and follows you into the annual return. Reconcile the two before you file the second one, not at the end of the year when the difference has repeated eleven times.
2. Claiming input tax credit that the supplier has not reported
Your credit depends on your supplier actually filing. A purchase invoice in your file is not enough. Check GSTR-2B every month, list the invoices that do not appear, and chase those suppliers while the amount is still small and the relationship is still warm.
3. Getting the place of supply wrong
This one is expensive. Charging CGST and SGST where IGST applied, or the reverse, means the tax was paid under the wrong head. Correcting it is not a simple adjustment. For services delivered remotely, the place of supply is not always where your office is, and it is worth confirming rather than assuming.
4. Ignoring reverse charge on ordinary expenses
Reverse charge is easy to forget because it attaches to everyday costs: goods transport, legal fees, sponsorship, some imports of services. The liability does not disappear because it was overlooked, and interest runs from the original due date.
5. Filing a nil return to stop the clock
When the books are not ready, filing nil to avoid the late fee feels sensible. It is not. A nil return that should have carried turnover is an incorrect return, and correcting it later costs more than the late fee would have. If you are going to be late, be late with the right numbers.
What to do about it
Almost all of this is solved by one habit: reconcile GSTR-1, GSTR-3B and GSTR-2B against your books every month, before filing rather than after. It takes an hour when the data is fresh, and it removes the reason most notices are issued.
If you would rather not run that check yourself, it is part of what we do for clients on a monthly GST retainer.