One acquaintance got into a somewhat-similar problem..
The explanation he received is along those lines;
- The booking website is not designed to check on health restrictions before accepting the booking.
- Some confirmed flights to highly-restricted destinations are zeroed in all classes, and the customer has to call and the informed agent will try to verify that he is allowed to fly and open space.
- For more standard flights, restrictions are checked before issuing the ticket based on all the information provided by the customer.
These procedures reduce the burden on the airport checking agent. As adambrau knowes, this is a very painful burden.

This is just hearsay,, so treat it as such.

But that would be consistent with the email message received by asia15. The call agent might have volunteered the cc explanation.But I would expect Visa to proceed with a prior verified by visa, so payment would have been rejected at booking.