Honouring fee whilst I have funds in the account

My business account has been with Standard Bank since 2015. I am being charged an honouring fee when I have funds in the account. I know for a fact that there is funds because I check that I have money in this specific account. 1) why does Standard Bank not sent an sms to let client's know of Bank charges 2) instead of saying declined "insufficient funds" Standard Bank let amounts go through and charge higher fees. 3) There is funds in the account, because I transferred, when I swiped I see a charge for honouring fee.

How many other clients has this happened to and they don't say anything?