What is the rule when import remittance and import invoice have different amount

Hi all,

Anyone have any idea to deal with following condition during import.

1. While remitting advance to a party in Singapore they took USD 50 over item amount of USD 500 as bank commission charges.

2. While shipping they had given an invoice of USD 500 which get in Indian customs with material and according BOE made mentioning invoice amount.

Do it will be okay to process it with banker by submitting relevant invoice and BOE or there is any formalities need to be done to match the both amount? 

What is the rule and regulation and how to deal with it??