1. The stronger defence is not simply "e-way bill was the supplier's responsibility" or "invoice value was below Rs. 50,000." That argument can be attacked if the department is actually questioning ITC eligibility.
Your response should separate e-way bill compliance from ITC conditions:
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ITC cannot ordinarily be denied merely because an e-way bill was not generated by the recipient. Establish that the purchases are genuine and supported by tax invoices, books, payment through banking channels, receipt of goods and corresponding accounting/GSTR-3B records.
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If individual consignments were below Rs. 50,000, explain the applicable e-way-bill requirement and why no recipient-side generation obligation arose.
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If the supplier generated the e-way bills, attach the e-way-bill data and reconcile invoice-wise.
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Most importantly, ask the department to identify the specific statutory condition for ITC allegedly violated. An e-way-bill discrepancy by itself should not automatically be converted into an ITC reversal.
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If goods were actually received and the supplier reported the invoices/paid the tax, demonstrate compliance with the applicable ITC conditions.
For ADT-02, I would avoid admitting that e-way bill generation was "not our responsibility" as a blanket proposition. Instead state that the audit objection does not establish failure of any statutory ITC condition, and provide invoice-wise reconciliation/evidence.