I faced this situation with a client and here are the steps, I did to resolve the issue. 

1. First I disabled Rules to auto add transaction in register. As a bookkeeper I found that rules setup in QBO is a best feature but sometimes it create a mess. So I setup rules without auto add transactions and I have control in review tab what is being categorized. 

2. Undo duplicate transactions. 

3. With in range from review tab, select all transactions and exclude those.

4. Delete from exclude tab, it is optional.