5 Common GST Filing Mistakes Small Businesses Should Avoid

GST · Harshit Dudeja & Co.

Small errors in GST returns can lead to notices, interest and blocked credit. These are the five we see most often.

1. Mismatch between GSTR-1 and GSTR-3B. Outward supplies in GSTR-3B come from GSTR-1, so fix GSTR-1 first and then check the tax you pay in GSTR-3B.
2. Claiming input tax credit that is not in GSTR-2B. Claim credit only for invoices that appear in your GSTR-2B, which means your supplier has reported them.
3. Wrong GSTIN, HSN/SAC code or tax rate on invoices. After the September 2025 rate changes, most goods and services are at 5% or 18%, with 40% for a few items. Old rates often stay in billing software, so please check.
4. Filing late. The late fee is ₹50 a day (₹20 a day for a nil return), subject to a cap that depends on your turnover. Interest at 18% a year is charged on tax paid late. Nil returns must be filed too.
5. Leaving returns pending for long. Notices have reply deadlines, and the GST portal does not accept GSTR-3B or GSTR-1 more than three years after the due date. Long non-filing can also lead to cancellation of registration.

A simple habit

Reconcile your purchase register with GSTR-2B every month before filing GSTR-3B. It catches most of these problems early.

Last verified: October 2026. GST rules and due dates can change, so please confirm before you act.