The Disbursement Report found in Blackbaud Merchant Services includes transactions processed online as well as transactions that were manually processed in the BBMS portal.
The Disbursement report is a canned report, we are not able to add or remove fields on this report. Currently there is no way to distinguish between the kinds of transactions in the Disbursement Report.
However, in a Transaction Search or Daily Transactions Report there is a field called 'Source' that defines if the transaction came in through a batch, card present, or card not present. Run a Transaction Search (in Transactions > Transaction Search) for the date range included in the appropriate Disbursement Cycle. These search results can then be exported from BBMS and compared those results of the Disbursement Report.