Thanks for sharing a screenshot, 2mandi2.
 

I could see that there are still amounts showing at the bottom. This tells me that you may not have linked the expense and the refund made to your customer. In your case I would recommend to use Credit Memo since this will affect customer's account. Then make sure to use Accounts receivable on the expense transaction. Once done, we can link these two transactions from the Receive Payment page. 

Also, you may need to check on the last payment you have recorded in QuickBooks. The status partial would tell that there is an amount left unapplied to an invoice. 

You can also check this article about Customer refund. 
 

Let us know if you need anything else.