Every funds transfer is one part expense, one part deposit. Our app tries to guess which transactions are transfers and lists them as "Possible Transfers" under Troubleshooting on the Transactions page. Simply tell us which are really transfers, and which aren't.
These items will remain as separate expenses and deposits until you mark them as transfers. If you are being prompted to categorize a transfer, that is because you have not combined that expense with its deposit.
Here's a video to help you out some more: http://quick.as/embed/89yirgg