Sounds like they made a mistake in their submission, rather than they wanted to ignore something or get an exception.

For such a large city with a huge amount of tax revenue, I would expect the bureaucracy in SF to do a little better with processes like this one. It would have been trivial to review these for required sections in advance or to give companies time to submit corrections. Obviously this isn’t how it works, like you stated “standard bureaucracy”, but I’d love to see certain parts of government move further away from this mentality of being some punishing Old Testament god to serving the community.