If a transaction that could not be transferred is sitting in your Connector you can set it on hold. This way, if you already entered it manually in your system you won't get double entries.
Open your Transaction Viewer:
After choosing Query you will see all transactions that could not be transferred (Status 44)
A click on the Status number 44 will show the reason for the failed transfer. Now choose the green Button "Reset Transfer Status".
The next step is to add the category Pre-ready to your query, by ticking the box and clicking Query a second time:
Next to the Status (probably 19 or 29 now) you now see the option to take an action (Hand symbol)
Clicking on the symbol will stop the transfer and the transaction will disappear. The transaction will be put into the category "User prevented Transfer", which contains all the "On Hold" transactions.