Welcome to the Community. Let's get this bank transaction issue sorted out and get you back to business.
First and foremost, QuickBooks reads the transactions exactly as they are sent from your bank. In this case, we'll need to exclude those transactions that were posted in reverse to avoid duplicates when re-downloading it.
From the left menu, select Banking.
On the Banking page, select the For Review tab.
Select the checkboxes of the transactions to exclude.
From the Batch actions drop-down, choose Exclude Selected.