FLY knows you purely by your booked name and the key is name plus passport number (to handle multiple names on the same booking). Now you can run into this problem if you had made two bookings for the flight - or the computer had somehow done this as a glitch I guess - but it doesn't do too much with API or nationality per se. And while FLY holds your passport details there isn't within Europe a validation of passport to the passenger as there is for the USA and South Africa. I wouldn't read too much into this, if it's the first time it's happened. The system isn't that clever and I doubt you will have massive problems going forward.