To pay rejection fee but not in arrears

My Telkom account should get debited every month but because I use the app I did an internet payment for the first two months. Now I get charged a rejection fee which is more then my monthly debit amount. The consultant told me that I should do internet payments ten days before the debit order is due for them not to try and deduct the monies. I understand that but then there should be a warning on the app. I'm being told to pay the rejection fee even though I'm not in arrears.