Yes! This is definitely happening with increased frequency. It happened to me three times since November, two times overseas. Once at checkin here in the USA, on a ticket booked 8 days out. Also in Johannesburg in November and in Cairo just two weeks ago. All cases were Delta metal, Delta check-in staff. I was allowed to board anyway, without card, maybe due to DM status.

On a related note, I was not allowed to board Ethiopian Airlines CAI-ADD for this reason! I had to purchase a new ticket on the spot. ET absolutely refused to hear my logic that this was a corporate travel purchase and I don't own the card! They cited security. Despite local assurances I'm still wrestling with them on the refund.

Concerning Delta, they have an unwritten policy that requires credit card be presented for travel originating in certain countries. I flew some employees to the USA this year and had to go in person to the airport counter to add notes to their files that card was physically presented. I only learned of the "policy" when I could not book travel originating in Africa online on delta.com.

The "policy" is supposed to affect only travel on tickets with travel originating in suspect countries, but is instead being misconstrued by staff to include all flights, even return legs. It's definitely a new risk, particularly to/from developing countries.