Hello there, athlet. This can happen if a customer has available credits and the Automatically apply credits feature is enabled.
QuickBooks will automatically apply for any outstanding credits once a new invoice is created for the same customer. You can unlink the payment to mark the invoice as unpaid.
Here's how:
Navigate the Sales tab and select Invoices.
Locate the invoice to open it.
Click the 1 payment made hyperlink below the PAID status.
Select the date, then remove the checkmark to the invoice to unlink the payment in the Receive Payment screen.
Tap Save and close to complete.
If you wish to disable the auto-apply feature, you can follow the steps below:
Go to the Gear icon and select Account and Settings.
Choose the Advanced tab.
Toggle the Automatically apply credits in the Automation section to disable it.