Every taxpayer has a particular format of the invoice maintained in their accounting system. In case of sale /supply, the tax invoice is designed and system generated. But for cross charge the format of tax invoice is not used and instead an excel format or FI module invoice is used which obviously differs in look and format. Hence, the officer has his doubt. Nothing to worry. You can explain the practical difficulties in maintaining the exact same format of invoice in both SD module and FI module of SAP, if you are following SAP. Otherwise, you check your accounting package and find out the fact of not having same format of invoice and reply to the officer accordingly.