I'd like to help, JosephSenese.
If you use both QuickBooks Online Banking and QuickBooks Payments, this might be the reason why you see duplicate transactions in your bank register. To clarify, did you add the other transaction from the Banking page? Make sure to only choose the one that fits your business.
With regard to the screenshot you've provided, I can see that the other fee is not reconciled. If this is the transaction added from the Banking page, you can remove it from your bank register by following these steps:
- Go to Transactions or Banking > Reviewed or Categorized tab.
- Find the fee and select it by putting a check mark on the box.
- Click the Undo button. This will add the transaction back to the For Review section.
Please see this sample screenshot for a visual guide:

If you haven't reconciled the account, you can use the steps provided by my colleague above. This helps to match transactions recorded in QuickBooks and the figures downloaded in the Banking page. For example, the original invoice was entered for $503, but the same transaction with the applied fee is downloaded as $500 on your bank statement. What you can do to match both is to create a bank deposit and include the fee to match them.
Here's a sample screenshot for reference:

For more details, you can go to the Include bank or processing fees section in this article: Record and make bank deposits in QuickBooks Online.
If you want to create a bank rule, the instructions can be found here: Setup bank rules to categorize online banking transactions in QuickBooks Online.
Please let me know if you have any follow-up questions. I'll be around to help you out again. Thanks.