You will need to provide more information. Are you processing credit cards through a third party? Was the double payment only in Sage 50? Was the card actually charged twice? How do you get the MasterCard transactions into Sage 50? Any thing else you can tell about your normal process without revealing personal information? 

Assuming you used the Pay Credit Card Bill option in the Payments module, you will have to post a General Journal entry to reverse the second payment.  There is no Adjust or Reverse button for credit card payments yet.