Company claiming more money for shortfall in notice period what to do

I was working for a MNC in Bangalore for from 13-Aug-2013 to 23-Jun-2017. I had resigned on 14-May-2017 and served notice period till 23-Jun-2017 and got relieved. I was in a hurry to join new job and hence I had requested them for early release and the same happened. But, now when I am seeing my Final settlement the company is asking to pay for the shortfall of notice period. As per the clause of notice period - its says - Employees must serve a notice period of 2 months and people working on critical projects has to extend another 30 days more ie., upto 90 days and the exact period of which will be communicated by the management. Now, as per this clause, I am saying them that the notice period is 60 days but not 90 days and hence I will pay the shortfall of 60 days. My company has a different opinion and they are quoting that notice period is 90 days and I have to pay shortfall for 90 days. Please suggest if I can go legally on this and win?