Appalling service and system

I made a booking online and received a confirmation and the funds were deducted from my credit card. I tried to check myself in numerous times but couldn't. Upon my arrival at the airport, I went to the check in counters and was told that I have to go to ticket sales where I was assisted by a lady by the name of Fikile Mnisi. I gave her full details of what was going on and she said there was nothing she could do because my payment still has to be verified by another department. I asked her to check with the manager to which she responded that there was nothing that they could do differently. I asked again and she pointed at her supervisor who was standing next to me and again insisted that he wouldn't be able to assist. Eventually she asked him and he actually assisted her. Ultimately they got my boarding pass but I had left my bag behind and has to run back to get it at which time the flight was closed on the system. I was scheduled to fly at 6am and was placed on the 8am flight, needless to say that I was extremely inconvenienced. Why do they permit bookings for early flights all night long if they can't be verified? No apology at all, I'll be shocked if they respond.