What credit card company did you use? These days several big name companies are employing extra security provedures, supplementary to the main payment, to validate your card. For example Mastercard has SecureCode.
However, none of these extra security features that I know of require you to fully enter your card details a second time. Would you be able to provide a screenshot (making sure NO personal information is displayed) showing the popup screen you saw? It would help in figuring out what it is that has popped up.