Deduction of Notice Period

I was employed with a company and had signed a employment contract with a notice period of 90 days. After 5 months of serving in the compnay, I resigned and requested a early relieving in next 30 days. The company did not accept or deny my resignation or relieving date. They did ask me to begin my transition of work to an existing employee. Within 15 days of my resignation the company sent me a exit email and sought me to complete the exit formalities. Now, in the F&F statement they are deducting notice period of 90-30 = 60 days and also paying me 30-15 days of notice period for their own shortfall. I am confused as they never asked me to serve the full notice period but is making this deduction. Is this right? What are my options? I have already sent multiple reminders and informed the company that if they has asked for notice period to be served in full or payment then I could have arranged it but they never mentioned and on the contrary it seemed that they were in a hurry to let me be relieved.