GST issue

Sir,
one customer raised the bill with hyderabad GST number with the deduction of SGST and CGST respectively @ 9% each.

At the time of payment to GST authorities, Customer paid with Delhi GST number with deduction of IGST @ 18% and invoice amount is not tallied with GST return amount.

Kindly guide me how to solve the issue.

With Regards,
K.VENKATESH KUMAR.