Flight left early or was overbooked - delayed honeymooners who were gifted flights to Durban

We have always booked with Flysafair due to their great service and friendly staff. So naturally when we gifted my brother a honeymoon for him and his bride we rushed to book with Flysafair. Tickets were booked on 5 July 2024 and paid online for 29 September 2024 to depart to their honeymoon. We dropped them off at OR Tambo early and they checked in a bag and proceeded to the ques. Firstly they were early and was ill informed by Flysafair staff of where to queue and landed up in a queue for a flight to go to cape town when they were booked for Durban. regardless of the unhelpful staff they were still early. Flight FA767 boarding time was 17:30, gates close 17:45 and departure was 18:00. my brother and his bride was at the airport queing by 17:15 ready to go, when they got to the front of the queue they were told they "missed their flight". after arguing and trying to find a resolution they were not helped. Time where this concluded was 17:28 (2 min before boarding was supposed to start). So the flight either left early which is obsurd, or the flights were over booked / double booked. So we were not furious with them being delayed to the next day as they were told to return at 3:30 the next morning to be placed on a waiting list for the next flights, this all was still fine and we understand things happen, however what is inappropriate in my opinion is that my brother was charged a fee of +-R600 to have the option of being placed on the waiting list the next morning. they did not "miss their flight" as they were on time and were told the flight had left before boarding was even to start, further, these tickets were booked 3 months in advance to ensure they have no delay to their honeymoon and we understand delays, but to charge someone for the failure of the airline i think is really sad. It really does make one question booking with you again