The provider shows the money taken, and the site has no order. An order is created when the checkout's invoice is fully paid, so start in the admin, under Invoices, with an invoice for that amount. A paid invoice whose source is a checkout means the payment reached the site; no invoice at all means it did not. Then, in order:

  1. The payment is still being confirmed. A payment that needs a 3-D Secure challenge, a redirect to the provider, or a confirmation that comes later, such as a bank debit, keeps its checkout, split from the cart, for up to a year (the Checkouts setting Standalone Checkout Lifetime). The order is created when the provider confirms the payment. Check the payment's status in the provider's dashboard, and see The payment-processing page and webhooks.
  2. Two payment attempts. A retry after the checkout changed opens a new invoice for the new total, and the order comes from the attempt whose invoice is open. When both attempts went through, for example a 3-D Secure challenge finished in another tab, refund the other payment from the provider's dashboard.
  3. PayPal. A PayPal payment completes inside the purchase call. Compare PayPal's transaction log with the site's orders to find a capture with no order, including one PayPal reports as pending.
  4. The order number template. Every order needs a number of its own, so the order number template must contain {SEQ} (Order numbers).
  5. It was a form payment. A payment element on a form creates an invoice and a transaction, never an order.
  6. The order is on another environment. Staging and production can share a provider account, and each has its own orders.

For the shopper, refund the payment from the provider's dashboard, or create the order through the orders API, and contact them either way. If none of these explains it, contact Core dna support with the invoice, the provider's payment id and the time.