I had this situation when I booked a ticket for myself and a friend. When I went to the airport for a different flight, I had them note the credit card for my friends flight and he didn't have any problems 3 months later when the flight actually was. However, I was asked for the credit card when I checked in because I forget to "clear" my flight earlier.
PS. When I booked the flight it indicated that the credit card would be needed at check in.