Dear Sumit, You have not mentioned the amount of the two PF deductions in your payslips. There are three main components (from the employer's point of view) in PF deduction and deposit: (1) Employee EPF Contribution (12%), (2) Employer EPF Contribution (12%), and (3) EPF Admin Charges (EDLI, Admin, etc. - 1.36%).
When the employer deposits the EPF, all the above amounts are deposited under different heads. Some companies also deduct the third type of deductions from the employee's salary (which should be deposited by the employer from their pocket). In some cases, it is noticed that ADMIN CHARGES are also deducted from the employee's salary.
If this is the case, as I am assuming, you can ask your employer not to do so. Being covered under EPFO, it is the responsibility of the employer to deposit the admin charges from the company account.
If you need more clarification, please share your salary figures and the amount of double deductions. The forum members will try their best to clarify the same.