About my baby's NSO birth certificate. Please reply.

My boyfriend is abroad when my child born.
And to be able to use his surname, i first register my child with my surname.
after that, my boyfriend made Affidavit to use surname and affidavit of acknowledgement and sent it here in the philippines with red ribbon from the consulate abroad, then
authenticate it here at dfa, then passed the AUSFw/redribbon, acknowledgementw/redribbon, my babys original birth certificate from local registrar, my nso birthcertificate and my boyfriend nso birth certificate to Manila City Hall. then after that,
Manila City hall give back a certification saying that the AUSF and acknowledgement been legalize and issued.
And they also said, that it's been to NSO also.
But 3 months after that. My baby's birth certificate in nso never change.

Is there any step we missed?

Bring all those documents again to Manila City Hall and show them the response they made saying that the acknowledgement has been legalized and issued. So they can verify if there's any processing has been done with it or not. I doubt you missed any processing if they have responded to you that it has been done. Someone must have forgotten to forward the necessary documents to NSO.