Full and final settlement

Hi, i was a contract employee to one of the mnc company under payroll XXX, later got converted has permanent employee to the same mnc company, i worked 9 months under my payroll company,company deducted my PF amount (both employee contribution and employer contribution) from my salary. Now the company is not ready to pay the Pf amount which was deducted from our salary, also PF account itself is not opened for us. When this issue was higlighted all of a sudden company is ready to open PF account, also they wanted us to pay extra amount for not serving notice period of 3 months completely. My question is when company HR acepted my resignation 6 months prior but when FNF came into picture he started digging all this. My offer letter says " company may at its sole discretion decide to relieve you from such date as it may deem fit even prior to the expiry of the notice period" . So should we still pay them anything for not serving 3 months of notice period? Can a company deduct both employee contribution and employer contribution from our salary itself? Kindly help..