We can fix this in no time turning off the Automatically apply credit feature. Let me show you how.
1. At the top right corner, click on the Gear icon.
2. Under Your Company, select Account and Settings.
3. Click Advanced on the left panel.
4. In the Automation section, click on the pencil icon.
5. Turn off the Automatically apply credits.
6. Click Save.
7. Click Done.
Please feel free to see the screenshots below to see exactly what I mean on turning off the Automatically apply credit.
Moving forward, your newly added invoices won't get automatically applied with the unapplied credits.
For the automatically paid invoice you have, let's go over it and detach (unlink) the old payment.
1. Open the Invoice.
2. Click on the payment link.
3. Select the payment you want to unlink.
4. Under Outstanding Transactions on the Receive Payment page, uncheck the invoice.
5. Click Save and close.
6. A prompt will appear. Click Yes to confirm the edit.
7. If applicable, repeat the steps for other invoices.