To reiterate what most have advised: Better to go to your permit office and simply explain the miscommunication, than risk corrective enforcement in the future...which could include demolition of what could be deemed an unlawful structure.
I didn't have a chance to read the entire article, however it appears the tenant has a good chance at winning a civil suit against the landlord...if he chooses to exercise that option.
I think sometimes we have a “No” or “You should already know this” culture. We have stations and that has helped, but nothing goes further, in my humble opinion, than a genuine willingness to assist! Customer Service is very underrated these days.