What Arrears???

I have been with Nedbank for many many years, when I querry the fees or any activity I have learnt that not much if nothing gets solved, I settled my loan account today. on the app it gave me a settlement amount, I could not pay it directly as my increased daily limit was not big enough so I called Nedbank and they said they could pay it directly for me as it was from my savings account. I was pleased and told them to go ahead. however to send me a letter to say that I settled it. long story short....they took off more than the settlement showed me on the app and I received a letter stating that I was in arrears. Not that I had paid the complete loan up. I have Never been in arrears and how will this now effect my future credibility with Nedbank? hopefully this too doesn't go onto my ITC. My app also says that I have some money due to me from my loan account however I can not access it.