Thanks for joining in this conversation, @codymeansy. It could be that that the Auto apply credit is turned on. 

Let's go to your Settings and turn it off so it won't affect your invoice. 

Here's how:

1. From the Settings menu, select Account and Settings.
2. Choose Advanced, then click the pencil icon under Automation.
3. Unmark Automatically apply credits option then hit Save once done.

Once done, let's open and unlink the payment for that specific invoice. Here's how:

1. Go to the Sales menu then select Invoices.
2. Choose the specific invoice with mark as paid and deposited.
3. Click payment made below the PAID payment status.
4. Uncheck that invoice to unlink to the payment.
5. Hit Save and Close once done.

For future reference, follow the steps to match your bank transaction with the one you've entered in QuickBooks in this help article: Match with an existing transaction. 

Visit us here again at any time if you have additional concerns. I'd be delighted to attend your next posts.