Regarding the fee issue - This happens all the time and you cannot do anything now but pay the pending fees. From seeing similar posts all over the internet, they don't budge how much ever you complain and if you don't pay, your cibil score takes a tumble. Better to settle it and close.
How did you submit the application? Was there an OTP involved?I raised a complaint but they are adamant that I was detailed and duly signed the application which obviously I never did.