Unfortunately there is no way to tell who processed a refund in the report data. Because of this refunds that you manually processed will show up in the Refunds report as a problem: "not reimb or returned".
There is, however, one way this can be remedied. We recently included a feature to import seller notes from the order detail page (for PC users).  If you don't already, when manually refunding a customer, be sure to put in a note to indicate that it was done by you. This way there will no confusion over what returns should be looked into.