Terrible Service Rendered

I paid my account via the banking app and there was no option to add the reference number. In a s much as I understand that this will have my payment roaming in the system, to have to wait for 3 weeks for this to be reallocated to my account is completely absurd. My connection has been disconnected and now seemingly I am have arrears that I might be accountable for. Customer Services cannot assist in any way and this was handed over to my account. How am i subjected to pay for inactive services with intermittent disconnections.