Legal query regarding purchase of resale property

I have bought the resale flat in pune.I have question that I have got position and the money is paid to the owner.I have final deed submitted in the bank for the same after loan process.I did initial deed in month of July to pay entire amount within 30 days but owner provided the all the documents to me after 25 days and hence loan process took next 45 days for payment .We did final agreement as I mentioned earlier and payment was done.But I need MSEB transfereed to my name .But owner is asking me 50K as penalty for late payment after giving full and final payment .What should be done in this case?Please suggest. Thanks .