If your customer has a credit balance on their account and you're not sure why, I recommend checking the payments linked to that customer's latest invoices and make sure there isn't a duplicate somewhere. If you find that there's a duplicate payment linked to one of the invoices, you can follow the steps below to delete it.
That's it! Now you can apply the existing correct payment to that invoice.
Just shoot me a reply if you run into any other questions. I'll be here to ensure your success.