I had not set up QuickBooks payments and customer paid online through invoice. Where is the money?

Welcome to the Community forum, hdearly187. I want to make sure you can receive your customer payment.

Since QuickBooks Payment hasn't been set up to receive invoice payments, I recommend reaching out to your customer to confirm the bank account they used for the payment. You can find more detailed guidance on receiving invoice payments in this article: Record invoice payments in QuickBooks Online.

For useful insights into your purchases, sales, and inventory status, take a look at this article on which reports to run: Use reports to see your sales and inventory status.

If you encounter any further concerns while using QuickBooks Online, don't hesitate to return to the Community. We're here to help, hdearly187!

You'll likely not get a good answer from the QuickBooks Team.  I'm going to encourage you to ask your customer to stop the payment that was submitted incorrectly and resubmit it correctly.  
Also, check your settings to make sure nothing has been accidentally turned on that allows this.  QuickBooks is horrible when it comes to resolving client payment issues. 

I hope you're able to get it resolved.