Start with the report period
Before comparing any number, confirm the order period and the payment coverage represented by the files. A payout can include activity from an earlier order period, and a recent order may settle later.
Separate the layers
Read the data in layers: orders placed, events that changed those orders, marketplace deductions, payment entries and the resulting settlement.
Use exceptions as a reading list
Returned, cancelled, RTO and unmatched records are the entries that deserve attention. Review them by order or SKU before drawing a conclusion from an aggregate.
Keep the source files
Keep marketplace statements and downloaded analysis together for the period you are reviewing.