Common GST Queries with Step-by-Step Resolutions (2025 Guide) | Simple Answers for Businesses & Taxpayers

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Goods and Services Tax (GST) has simplified indirect taxation in India, but daily compliance tasks such as invoicing, return filing, reconciliation, e-invoicing, and ITC claims often lead to confusion. Whether you are a business owner, accountant, or GST practitioner, understanding common GST issues and resolving them quickly is essential for smooth operations and avoiding penalties.

This comprehensive, non-copyrighted 6-minute guide covers the most frequently asked GST queries along with easy, step-by-step solutions that you can implement immediately.

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 Why GST Queries Are Common?

GST is dynamic — rules, formats, and reporting requirements change frequently. Businesses face challenges due to:

• Filing errors
• Wrong classification
• Mismatch in GSTR data
• Delayed or incorrect ITC
• E-invoice & e-way bill issues
• Portal glitches

Having clear answers helps improve compliance and reduces financial risks.

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 1. Query: Why is my ITC not reflecting in GSTR-2B?

Possible Reasons

• Supplier has not filed GSTR-1
• Supplier filed invoice under wrong GSTIN
• Incorrect invoice number/date
• Tax mismatch between supplier invoice & portal
• Invoice uploaded in the wrong month

Step-by-Step Resolution

1. Open GSTR-2B and identify missing invoices
2. Contact supplier and request them to file/update GSTR-1
3. Ensure invoice details (GSTIN, date, number, value, tax) are correct
4. Accept ITC only when it appears in GSTR-2B
5. Track status using Communication with Taxpayers on GST portal

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 2. Query: How to resolve GSTR-1 vs GSTR-3B mismatch?

Reasons for mismatch

• Taxable value difference
• IGST vs CGST/SGST wrong selection
• Credit/debit notes missed
• B2B shown as B2C or vice versa

Step-by-Step Resolution

1. Download GSTR-1 summary from the portal
2. Compare with GSTR-3B tax liability
3. Identify month-wise difference
4. Amend invoices in next month’s GSTR-1
5. Pay additional tax liability if needed using DRC-03

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 3. Query: Why is the GST portal showing “Invoice Already Exists”?

Causes

• Duplicate invoice number
• Supplier uploaded invoice twice
• Wrong financial year selected

Step-by-Step Resolution

1. Check whether the invoice already exists in GSTR-1 → B2B
2. Change invoice number if needed
3. Ensure correct period is selected before uploading
4. Delete duplicate invoice entries

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4. Query: How to fix “Invalid HSN Code” error?

Possible Reasons

• Wrong number of digits (4/6-digit mismatch)
• Incorrect HSN mapping for the product
• Excel upload format error

Step-by-Step Resolution

1. Verify HSN using GST HSN Lookup
2. Use 6-digit HSN for turnover above ₹5 crore
3. Ensure no space or extra character in the HSN field
4. Correct format and re-upload

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 5. Query: GSTR-3B shows negative liability — what to do?

Main Causes

• Excess ITC reported earlier
• Liability paid twice
• Amendments in previous periods

Step-by-Step Resolution

1. Verify previous GSTR-3B filings
2. Check ITC reversal (Rule 42/43)
3. Adjust negative liability in next month’s filing
4. Keep working notes for audit trail

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 6. Query: How to correct wrong GSTIN entered in sales invoice?

Step-by-Step Resolution

1. Create a credit note against the wrong invoice
2. Issue a new invoice with the correct GSTIN
3. Report both documents in GSTR-1
4. Ensure corrected invoice appears in customer’s GSTR-2B

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 7. Query: E-Invoice generated but invoice not showing on portal

Reasons

• IRN generated but not synced
• Portal cache delay
• Wrong document type

Step-by-Step Resolution

1. Check e-invoice portal for IRN Status
2. Verify using IRN, Ack No., or Date
3. Re-upload invoice if status is failed
4. If signed JSON exists → invoice is valid even if portal delays

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 8. Query: E-Way Bill showing “Part B Not Filled”

Step-by-Step Resolution

1. Login to ewaybillgst.gov.in
2. Open generated e-way bill
3. Enter vehicle number in Part B
4. Update transporter details if required
5. Print updated copy for movement

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 9. Query: How to claim ITC on reverse charge (RCM)?

Step-by-Step Resolution

1. Pay RCM tax through GSTR-3B – Table 3.1(d)
2. Claim ITC in the same return under Table 4(A)(3)
3. Maintain proof of RCM payment
4. ITC is allowed only on business-related services

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 10. Query: GST return filing error – “Invalid JSON”

Solutions

1. Re-download the latest offline tool
2. Remove special characters (%, &, *, #)
3. Validate sheet before generating JSON
4. Avoid merging cells in Excel
5. Upload again

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 11. Query: How to revise GST returns?

GST returns cannot be revised, but you can correct mistakes.

Step-by-Step Resolution

1. Make amendments in next GSTR-1 (Table 9/10/11)
2. Adjust liability or ITC in current GSTR-3B
3. Maintain reconciliation records

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 12. Query: Supplier filed invoice late. Can ITC still be claimed?

Answer

Yes — as long as the invoice appears in GSTR-2B of the relevant financial year as per current rules.

You must not claim ITC manually if it is missing from 2B.

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 13. Query: How to fix GST login “Wrong Username/Password”?

Solutions

1. Use Forgot Username or Forgot Password
2. Check registered mobile/email
3. Clear browser cache
4. Prefer Chrome/Edge browsers

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 Best Practices to Avoid GST Issues

• Reconcile GSTR-2B with Purchase Register monthly
• File GSTR-1 before 11th to avoid mismatch
• Use correct HSN/SAC codes
• Maintain digital records of invoices
• Use GST-compliant software like Tally Prime
• Track ITC eligibility rules frequently
• Avoid handwritten invoices

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 Final Thoughts

GST compliance becomes easy when you understand common issues and follow step-by-step resolutions. Most problems arise due to incorrect data entry, mismatched records, or delays in supplier filings. By staying updated, reconciling regularly, and using digital tools, businesses can ensure:

✔ Smooth GST filing
✔ Higher ITC accuracy
✔ Fewer notices
✔ Better audit readiness

This guide helps you resolve the most frequent GST queries quickly, accurately, and confidently.

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