You can have unhappiness much more than size of the city, all unhappy from urbanization can exceed number of citizens. In late game when you conquer many cities, unhappiness from other sources equals to number of citizens and many of my newly conquered cities for many turns unhappy more than their size.
We mentioned that one case already, urbanization comes from specialists. That is as far as I know the only way you can breach the floor of unhappiness. If you conquer a new city they will, or I have never seen, a city with more unhappiness then their size. If you see that I can only imagine that it must be specialists assigned -- which you should never let the AI do or control.