There are multiple reasons why your invoices are showing up as paid. These includes:
Another user of the account may be adding the payments to the invoices.
If you have a Payments account, you could be sending that invoice to the customer by pressing Save and Send rather than Save and Close.
Note: When sending an invoice to a customer, there is a link to pay the invoice once you have a Payments account.
Let's check the Audit Log to see if someone made the changes within the QuickBooks account:
Go to the Gear icon in the top right-hand corner.
Under Tools, select Audit Log.
Under User, select AllUsers.
Filter the date as to when you created the invoice.
Under Events, choose All transactions.
If you don't see any information here, provide me with a screenshot of the invoice so I can determine the best solution for your business.
Another reason to consider is their credit. Instead of a refund, some customers prefer getting a credit they can use to reduce the balance on their next invoice. To verify if this feature was turned on, you can follow these steps:
From the Gear icon, select Accountandsettings.
Go to the Advanced tab.
Click the edit (pencil) icon on the Automation section.
If the Automatically apply credit button is green, it means it's enabled. Otherwise, it's disabled.