Inefficient Cheque account IT systems

I have a Nedbank Professional Banking Cheque account where I receive my salary every month. I find that when I swipe my card at merchants the card allows the purchase if there is money in my account. However, I find that usually, the balance on my account is never enough to cover all purchases made. Nedbank then charges me R90 for all the transactions above the balance I had in my account but it is a problem with the merchants and their system and no fault of mine.

The worst part is on 4/12/2018, I had a debit order of R530 going off my account. I had a deposit of R600 done from an Absa account. Despite my telling the relationship officer that there was a deposit of R600 that was going to offset this R530 she still returned my debit order and charged me R90 for the transaction. I think Nedbank, needs to invest in better IT systems.