Kotak Mahindra - Cheque dishonoured due to bank's mistake.

This is regarding my Kotak bank personal loan of 60k. I have had few delays in payment but never defaulted on any emi's. I have made payment of some 20k in Nov 2016 thinking thats the final closure amount but the bank came back to me in march saying that it was not final amount. There were some overdue charges of 20k which after negotiating with them on 18th July they came back asking me to make payment of 10727 as final closure amount. I made 2827 through NEFT n balance 7900 through cheque which was deposited in their branch on 31-7-17. But due to mistake of bank the cheque was not cleared (bank executives said its wrong loan no. which was actually right loan no.) and until 14th August they have not even informed me even after i wrote zillions of mails and calls asking them for the status. After that they even charges me bounce charges for their mistake. Now after writing mails and calling whole kotak team including the CEO, Country head have made payment through NEFT. But the bank has charges me extra charges for the mistake of theirs. Please guide what should be my next step as their mistake is costing my financial score.