UNREASONABLE BANK CHARGES AND appalling SERVICE

I have a standard bank Cheque account I recently discovered certain charges that do not make sense, I made a purchase at Nandos of 139 to be exact transaction went through unbeknown to me the transaction was outstanding 3 or 4 days later the merchant(Nandos) banked it. So normally in a situation like this I would be on a negative (negative the amount you weren't over with) in this case it should be -139.00, So Standard charged me an honoring fee of 130.00 over and above, having to pay 269.00 , I called the Standard bank call centre to enquire what this honoring fee is for and was told that I am basically paying this amount because standard bank paid this transaction on my behalf because my account did not have any funds,My question here is why do I have to pay double and also it's not my fault that their systems are still backwards where it takes a merchant more than 3 days to bank off their money aand also its not like at the time of transaction there were no funds in my account. I really find this unacceptable because when these sales people call you to open a cheque account they don't tell us such things otherwise I wouldn't have stayed with them.