If any employee joins to the company on or after 1-Sep-2014( he is enrolling to PF for the first time) and his basic salary is more than 15000, he would not be eligible for EPS, the entire amount will go the Employer PF.
However, if the employee had the PF in the previous company then EPS has to get deducted. Request you to enable "Is existing member of EPS" option if he already enrolled to that EPS will get deducted. Please find the below path for the same.
Employee> information>> PF/bank/details> edit>select employee> Enable "Is existing member of EPS" option> save and process the salary.