Same thing happened to me couple of years ago in BKK with PG. They simply asked me to pay the same fare with cash or (other) cc at their counter and reimbursed me the original cc payment within few weeks. They were somehow apologetic about it and handled the whole thing promptly.

Especially with Asian carriers I'm frequently asked to show the cc used for the payment. I have not seen any consistence though, meaning even the same airline might ask today but not on my next trip.