GST Filing Problems & Solutions (2025 Guide)
A step‑by‑step, problem‑solving handbook for GSTR‑1, GSTR‑3B, GSTR‑2B reconciliation, ITC eligibility, e‑invoicing, RCM, and portal pitfalls — with checklists, examples, and FAQs.
GST Filing Overview
At its core, GST compliance rests on three pillars: accurate outward reporting (GSTR‑1), correct tax payment and return (GSTR‑3B), and eligible input tax credit based on GSTR‑2B. Errors usually stem from timing differences, wrong tax heads, or vendor non‑compliance.
- Monthly cycle: Reconcile sales ledgers ↔ GSTR‑1 ↔ e‑invoices; Reconcile purchase ledgers ↔ GSTR‑2B; File 3B with correct net cash liability.
- Quarterly filers: Remember IFF vs full GSTR‑1 and how 2B is generated.
- Golden rule: If it isn’t in 2B, don’t claim ITC.
Fix GSTR‑1 ↔ GSTR‑3B Mismatch
Step‑by‑Step Resolution
- Download period‑wise GSTR‑1 summary and 3B summary. Export sales ledger from your ERP for the same period.
- Match taxable value and tax head (IGST/CGST/SGST). Identify invoices missing/duplicated or reported under wrong POS.
- Use Amendment Tables in GSTR‑1 to correct wrong GSTIN, POS, values, or to add missing invoices.
- Adjust liability/ITC in the next GSTR‑3B with a clear audit note. Never back‑date invoices.
- Maintain a Mismatch Register to track carry‑forward corrections month‑on‑month.
GSTR‑2B Reconciliation & ITC Rules
GSTR‑2B is a static statement — your ITC should align to it. Any invoice missing in 2B is a red flag.
| Problem | Root Cause | Fix |
|---|---|---|
| Invoice not in 2B | Supplier didn’t file GSTR‑1 or used wrong GSTIN/POS | Follow up; get a correct amendment; claim ITC only after it appears in 2B |
| Blocked ITC | Personal use, motor vehicles, food/beverages, club memberships, etc. | Do not claim; maintain a blocked‑ITC ledger |
| 180‑day payment rule | Vendor not paid within 180 days | Reverse ITC with interest; re‑avail upon payment |
| RCM credits missing | RCM liability paid in cash but ITC not availed | Avail ITC of RCM in the same/next 3B (subject to law) |
Reverse Charge Mechanism (RCM)
Under RCM, the recipient pays tax. Typical cases: GTA services, legal services, import of services, certain notified goods. Key controls:
- Book RCM liability in cash in 3B; take ITC of the same in eligible head.
- Maintain a RCM register with vendor name, nature of supply, tax rate, and supporting documents.
- Ensure self‑invoice payment for unregistered suppliers where required.
Late Fee & Interest — How to Calculate
Two separate components apply:
- Interest on net cash tax liability for the number of days delayed.
- Late fee per return per day (lower for NIL returns) up to a notified cap.
Wrong Challan/Utilization Correction
Paid IGST instead of CGST+SGST? Utilized wrong head? Practical fixes:
- Set off correctly in the next 3B and adjust cash payment accordingly.
- Where enabled, request transfer between cash ledgers using prescribed PMT forms.
- Document internal approvals; attach to your working papers.
E‑Invoicing & QR/IRN Errors
E‑invoicing is mandatory beyond notified turnover thresholds. Common mistakes:
- Wrong GSTIN/ship‑to → leads to wrong POS and tax head.
- Missing IRN/QR on invoice shared with customer/logistics.
- Wrong HSN causing rate mismatch.
Fix It Fast
- Cancel IRN within the allowed window and regenerate with correct details.
- Reissue the tax invoice with valid IRN/QR before movement of goods.
- Automate HSN mapping and validation rules in ERP.
Amendments: B2B, Credit/Debit Notes, POS, HSN
Use amendment tables in GSTR‑1 for:
- Wrong GSTIN/Place of Supply: Amend original invoice period; do not duplicate.
- Value/Tax errors: Issue credit/debit notes referencing the original invoice.
- HSN corrections: Keep an HSN Master; amend descriptions to match classification.
NIL/Quarterly Returns & Missed Months
Missed filing creates a cascade of issues (blocking of e‑way, 2B generation). Recovery plan:
- File pending GSTR‑1/3B in chronological order with correct late fee/interest.
- If no transactions, file NIL return promptly to avoid penalties.
- Switching to QRMP? Understand IFF vs quarterly GSTR‑1 to avoid 2B gaps for customers.
Exports, LUT, and Refund Pitfalls
- Export under LUT without payment of tax: renew LUT annually; maintain shipping bills, FIRC/BRC.
- Export with payment of tax and claim refund: reconcile shipping bills ↔ GSTR‑1 (Table 6A) ↔ ICEGATE.
- Inverted duty refund: prepare input/output rate working; exclude blocked credits.
Portal Errors & Practical Workarounds
When the GST portal throws errors (time‑outs, validation failures):
- Clear browser cache; try another browser or system time sync.
- Download JSON, validate offline (where tools exist), and re‑upload.
- Keep screenshots of errors with timestamp; raise a ticket and attach to compliance file.
One‑Page Checklists
Monthly GST Closing
- Books ↔ GSTR‑1 ↔ E‑invoice register matched
- GSTR‑2B vs purchase register matched; pending ITC list updated
- RCM computed and paid in cash; ITC availed
- Interest/late fee computation sheet prepared
- Approvals documented; return filed and ARN saved
Vendor Management
- Share 2B‑pending report with vendors by the 10th
- Insist on correct HSN, POS, GSTIN on all invoices
- Contract clause for compliance & indemnity on ITC loss
FAQs
1) Can I claim ITC if my supplier hasn’t filed GSTR‑1?
No. Wait until the invoice reflects in GSTR‑2B, else risk reversal with interest.
2) What if I paid IGST instead of CGST/SGST?
Adjust via proper utilization in the next return and document the basis; explore ledger transfer where notified.
3) How long can I amend an outward invoice?
Amend within statutory timelines for that financial year’s returns. Keep customer acknowledgement for POS/values changed.
4) Is e‑invoice mandatory for me?
Check the latest turnover threshold and notification. If applicable, ensure IRN/QR on invoices before dispatch.
5) How to treat advances for services?
Tax is generally payable on receipt of advance for services; adjust on invoice issuance.
6) Can I carry forward unutilized ITC due to restriction?
Yes, eligible ITC can be carried forward; ensure not blocked and backed by documents.