I hope any company pays a salary for the past worked month. At the first point, you pay for the worked period, am I correct? (If you have any contract bond, that case is different.)
PF & Gratuity
These are the amounts which an employee saves at the employer's behest (as per Statutory Gratuity, it will also be considered as social security savings). So, you have to pay all these to him as per statutory norms. However, many companies still stop PF & Gratuity of employees for very silly reasons. The less knowledgeable ex-employees make rounds or else they come to your doorstep, but if any knowledgeable person or anyone with power can proceed against you legally. Finally, you cannot recover any amount from the employee's Gratuity legally (if, by any chance, any big legal case happens in front of the court of law and the court passes any sentence)... there are so many illegal moves which everyone knows.