@Diane26, we are also in San Francisco.
Often these things come down to the details, and your posting is a bit short on detail at the moment.
(I don't know if you are at liberty to share any of it.)
The Office of Short Term Rentals can be either very easy to work with, or a complete bear.
My experience was very good, and the person who helped me was very friendly.
Other people have told tales of inflexible people making their life difficult.
Did they say exactly what made your listing not qualified for a certificate?