In overall,
Condor has a fault that their system hasn't verified that the passengers didn't have the necessary travel documents.
I didn't get an answer from the OP for this question;
I really wonder if the traveler did check-in online or not? Did he/she succeed checking online if attempted?
So, I would assume that the check-in agent has manually entered the passport information to the system.
However, this does not mean that the passenger is able to fly because of the fault of the airline's web system or the check-in agents fault. It's always the responsibility of the passenger to have the valid travel documents and it's the airline's job to verify if they have the necessary documents for their travel.