I have the same issue. When I open my qbo and go to the "accounting" tab then "reconcile" tab and open the bank account to reconcile there are old transactions both deposits and withdrawals. Most are duplicates. I see in the "bank register" that there is no "r" next to them, but either a "c" or nothing. 

This is not in the banking, then for review tab. I do not need to exclude. This is in the actual reconciliation window.  I was told NOT to delete these transactions even if they are duplicates because it will mess up everything in the books, however these duplicate transactions are messing up the books by keeping them because the statement ending balance and the register balance for each month of the reconciliations report is off by these old duplicate transactions. 

QBO is showing some as manually added and then added by quickbooks. 

What is an easy fix?