The first place to check is in the ‘History’ tab of the booking - this details everything that has happened to the booking with the date and time when any changes were made/payments taken etc. so check here to see if the same payment is listed as having been taken twice.
You can also check your Messages section where there will be a record of the ‘Payment Received’ email.
In your Reports > Customer Payments > if you know the period of time in which the payment you suspect was taken you can search for any payments taken between that time frame. Do check this section to see whether the payment has been taken.
If the customer can already see the transaction on their bank statement then obviously this will clear up the issue. In the Booking > Payments > there is the Refund function which you can use to refund the customer the necessary amount.If clarification is still needed please contact us at firstname.lastname@example.org and we can check it with our payment system, Stripe.