Online car booking money making scheme

I made a booking online with Dollar thrifty (turns out then it was Carflexi) the booking was confirmed by e-mail and sms (CFF401ED). At the desk of Dollar Thrifty Cape Town Airport they sent me to Hertz as this did not march their booking numbers. There I filled all the necessary papers and rented a car for five days. After all the payments were done by Hertz on the credit card on my return (R2196.72), it turns out that Carflexi also took their amount of R636.36. Booking date 4 January 2019; car hire date 7 January 2019. When I phoned Hertz they confirmed that everything I owed was paid and also confirmed that the amount of R636.36 is not their's but Carflexi's. On my third enquiry to Carflexi I was answered that Hertz is their sister company and that everything is in order. I don't think so? I have requested the funds to be reversed or explained and I have not received any answer back on this matter.