In looking for the birth certificate of a great aunt I also found the
certificate number in the index followed by an S (special). The
certificate was on a different roll of microfilm at Bureau of Vital
Statistics in NYC.
There was probably no certificate filed at her birth and when one was
needed for her for whatever reason the proper proof as to her identity was
produced (ie an affidavit attesting to her name date of birth etc) and one
was given made out and given to her.