State Bank Of India [SBI] — loan irregular payment

I have taken a car loan in januar, 2017. My account has not been linked and the manager had asked me to submit cheques using which he will withdraw the money. The amount is not regularly deducted by him and i have to suffer because of it as late fees, when i asked him why extra amount has been deducted he has stalled me by saying that money will be refunded in a month or so. Now again emi are due and the amount has been increased. I have registered a complaint previously also but no satisfactory action was taken in reagrds to the matter.