My observations are:
Provident Fund Contributions After September 2014
You joined the company after September 2014. Since your salary at the time of joining was more than Rs 15,000, you were not entitled to the Pension scheme of the Provident Fund. Hence, the employer's contribution of 12% was remitted solely to PF without bifurcating it as 8.33% to the Pension fund and 3.67% in PF.
Remedy
You have to personally visit the EPFO Office and provide clarification that since you joined after 1st September 2014, you were not covered by the Pension scheme, and that is why the contribution to EPS is absent.
These are some of the issues with the EPFO in recent times. They created the law that those who joined after a certain date with a salary above a certain amount (say, Rs 15,000) should not be part of the Pension Scheme. Their system should capture all these and do the needful by itself without disturbing the members. However, they will not do it because their policy seems to be employee harassment.