Passport application of child

Dear Friends
My child was born in India. We applied for his passport after successful citizenship application. Today I received phone call from HMPO asking that my sons name is not on his birth certificate. The son is now 12 years old. We have used the same birth certificate for his Indian Passport all visa application and citizenship application. Birth certificate was made immediately after his birth so the name is not on the certificate. I explained all these details to the lady from HMPO on phone. Does anybody had similar experience and what can I expect further. I will appreciate any response to my query.