Most GST notices we see aren’t from fraud — they’re from small, avoidable mistakes that pile up over a few filing cycles until the department flags them. If you’re managing GST yourself, or even if you have someone handling it part-time, these are the five errors we run into most often when we take over a new client’s compliance.
1. Mismatched GSTR-1 and GSTR-3B Figures
Your GSTR-1 reports outward supplies in detail, while GSTR-3B is a summary return with tax payment. When the total outward supply figure in your GSTR-3B doesn’t match what you’ve reported in GSTR-1 for the same period, the system flags it automatically. This usually happens when businesses update sales records after filing GSTR-1 but forget to reflect the same numbers in GSTR-3B, or when different people handle the two returns without cross-checking.
The fix is simple in theory — reconcile both returns before submission, every single month — but in practice, this is exactly the kind of task that gets skipped when you’re busy running the actual business. Our GST return filing service builds this reconciliation into every filing cycle so mismatches don’t happen in the first place.
2. Claiming ITC Without GSTR-2B Reconciliation
Input Tax Credit (ITC) is one of the biggest sources of GST notices. Since the introduction of GSTR-2B, your ITC claim is supposed to match what your vendors have reported in their own returns. If a vendor hasn’t filed on time, or has filed incorrectly, your credit claim can get blocked or reversed — even though you paid the GST correctly on your end.
This is frustrating because it’s often not your mistake at all, but you still bear the consequence. Rule 36(4) under the CGST Rules restricts ITC claims to what appears in GSTR-2B, so reconciling before you file — not after a notice arrives — is the only real protection.
3. Missing E-Way Bills on Eligible Transactions
Any movement of goods above the prescribed value threshold requires an e-way bill, regardless of whether it’s a sale, a stock transfer, or even a return. Businesses that deal with physical goods — traders, manufacturers, e-commerce sellers — often miss this on smaller or “routine” shipments, assuming it doesn’t apply. It does, and the penalty for goods in transit without a valid e-way bill can be steep, sometimes leading to detention of the goods themselves.
If your business regularly moves inventory, this needs to be baked into your dispatch process, not treated as an afterthought.
4. Wrong HSN/SAC Codes
Every product and service under GST is classified under an HSN (goods) or SAC (services) code, which determines the applicable tax rate. Using the wrong code — even unintentionally — can mean you’ve been charging or paying the wrong rate of tax for months before anyone notices. It also flags your return for review if your reported code doesn’t align with what similar businesses in your category typically use.
This is especially common for businesses that sell a mix of products across categories, or that have expanded their product range without updating their billing software’s default codes.
5. Filing NIL Returns Late
Even in a month where you’ve had zero sales or zero purchases, you’re still required to file a NIL return by the due date. A lot of businesses assume that “nothing to report” means “nothing to file,” but the GST portal doesn’t see it that way — late fees apply exactly the same as they would for a return with actual transactions.
This is one of the easiest mistakes to avoid, and also one of the most common, because it’s easy to deprioritize a filing you assume doesn’t matter.
Building a Habit That Prevents All Five
Every mistake on this list traces back to the same root cause: reconciliation happening too late, or not at all. A monthly reconciliation habit — checking GSTR-1 against GSTR-3B, checking ITC against GSTR-2B, verifying HSN codes, confirming e-way bills for the month — catches almost all of these before they become a notice.
If you’d rather not track this yourself every month, check our GST & ITR due dates page to see what’s coming up, or talk to our team about taking GST compliance off your plate entirely.
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