Here is my take on what happened: The invoice submitted had different structure to the proforma invoice (list of items expected/agreed upon on the invoice). The customer is asking the supplier to explain the difference between the total of the submitted invoice and the amount expected if the proforma was used... Often a contract stipulates items that can be included on invoices, and amounts allowed to be charged for each item. If suppliers choose to go outside these agreed proforma invoices they need to explain why and how it happened - the total of submitted invoice is obviously higher than expected :-)
A better and clearer explanation is not possible without having access to the actual documents...