How is it even possible that this program allows duplicate invoice numbers?

Hello, @dave_thompson.

Currently, there isn't an option in place to warn if a duplicate customer invoice number is used in QuickBooks Self-Employed if you manually enter them. The invoices in QuickBooks Self-Employed are for tracking purposes only and they don't affect your business and tax reports. 

For now, you can manually track the invoice transactions and edit the invoice number. To do so, please refer to these steps:

1. Go to the Invoices menu.
2. Look for the Invoice you need to edit, click it and select Edit Invoice.
3. In the Invoice no. box enter the correct invoice number.
4. Click Save as draft or Send invoice.

I’m also adding an article that provides an overview of the Invoice feature. It includes instructions on how to customize the sales template, turn on the payments option, etc.: Create invoices in QuickBooks Self-Employed.

Also, when you receive the invoice payments, make sure to track them under the Transactions page. You can use this link for more information: Manually add transactions in QuickBooks Self-Employed.

In case you need to set your numbering preference, you can use the  Custom transaction numbers feature in QuickBooks Online. This adds an Invoice no. field where you can enter any number or letter format you want and the sequence you set here applies to all sales forms: How to change the invoice number on sales forms.

If you have further questions about invoices in QBSE, please leave a reply below. I'll be always around to help. More power to your business. 

Thank you for the prompt reply, @Kelly_T. I appreciate the details you included in your post. I'll help you out with this concern. 

You can follow the suggestion by my peer @DivinaMercy_N above, which is to run the Verify and Rebuild Data tools. 

In case you missed it, here's how to Verify Data:

1. Go to the File menu.
2. Highlight Utilities, then select Verify Data.

If the tool detects any data damage, proceed with Rebuild Data:

1. Click the File menu.
2. Highlight Utilities, then select Verify Data.

Check out this article for more information about resolving this type of situation: Resolve Potential Data Issues in QuickBooks Desktop. 

If you continue to experience the same issue after running the tools above, feel free to contact our Technical Support team for further assistance. They can pull up your account within a secure environment and investigate this issue for you. Please take note of their operating hours, so you know when they're available. 

Don't hesitate to leave a comment below if you have other concerns with duplicate invoices in QBDT. I'll be sure to get back to you. Have a great day!