Unreasonable charges made at clients expense

I have a business account with FNB since 2013 November which everything went well until just recently when im being charged for things i do not know,my bank charges seem to exceed R400 every month and this month its worse.Right now my acc is in -R604.02 the ref being #Excess item fee so there first one is R135 the second is R240.i called and spoke to Mayline May on *** and she says those charges are for transactions that i made but they took time to be banked hence my account went on access....whose fault is that? when i have money in my account and swipe i do get notifications that the transactions has went through so now who is to pay this R604.02? this is just unfair for FNB to do. And i have a personal account of which this month my charges are lower than usual,i make sure i use FNB ATM's but the charges still shoot up and im not the firt to complain even on the FNB facebook page something really needs to be done otherwise FNB will lose customers.