It's important to mark transfers properly to avoid recognizing incorrect income and incorrect expenses. That happens when transfers aren't marked because every fund transfer is one part expense, one part deposit. So if you have a transfer from one account to the another for $10,000, but didn't mark it properly, you will have:
$10,000 income that isn't actual income
and a $10,000 expense that isn't an actual expense
Our app tries to guess which transactions are transfers and lists them as Possible Transfers under Troubleshooting in the Transactions page. Simply tell us which are really transfers, and which aren't. Remember that these items will remain as separate expenses and deposits until you mark them as transfers.