Extremely poor customer service

Myself and my girlfriend were booked on flight FA1002 to Cape Town this morning but were 5 minutes too late to check in as we were struggling with the self service. We both understand we were late and there are rules that must be followed by your staff. I was very upset as we were being told we had to pay R1200 which to us as students is a lot of money, my complaint however is not about having to pay this fee