During a war against Venice I captured one city state that it had turned into a puppet. I found that the liberate option did not appear so I turned it into a puppet state. I then demanded another of Venice's puppets, Genoa, as part of the peace treaty and again the liberate option did not appear, so this city also became a puppet. There seems to be no way to liberate these two cities. I checked the city screens and tested annexation (then reload). The cities are still in a state of civil unrest though. Is this a bug or did something else go wrong? Having them as puppets is not too big of an issue, but I am playing as Ethiopia so this may count against the UA bonus.