Stripe.com payment integration module

[Gozzandes]

We had a customer place an order with Visa. It is listed as "Succeeded" on Stripe, but no order in Zen. A few minutes later, the customer altered his order and then used Link to Pay, which was also "Succeeded". This 2nd order was received in Zen. The customer brought this to our attention claiming he was double charged....
How can a transaction succeed at Stripe but not show up in Zen?

Looking into it further, the Visa is listed as originating from South Africa. The Link transaction, is in USD and was shipped to a USA address.
I hesitate to refund the Visa order as it feels like it could be a Scam of some sort...some loophole in Stripe.

Payment succeeded information is sent from Stripe server after clicking "Confirmation" button.
and
includes/checkout.js receive the information and show payment succeeded message and click order confirmation page button.
line 48-50 and 69-71
It may be better to click first the order confirmation page button.
from

      document.getElementById('checkoutConfirmDefaultHeading').textContent = PaymentSuccess;
      showMessage(PaymentSuccess);
      document.getElementById("btn_submit").click();

to

      document.getElementById("btn_submit").click();
      document.getElementById('checkoutConfirmDefaultHeading').textContent = PaymentSuccess;
      showMessage(PaymentSuccess);