I think this is not a bug. Let me explain.
As far as I know, it's not a matter of who owns the city: the cities that can be target of a crusade are set in data\world\maps\base\descr_regions.txt, where you can find a list of every city with the tag "crusade" below. Without that tag, no crusade is possible for a given settlement.
Code:
Jerusalem_Province
Jerusalem
egypt
Arab_Rebels
244 13 29
crusade, jihad, horde_target, jerusalem, holyland
5
4
religions { catholic 2 orthodox 48 islam 35 pagan 0 heretic 15 }
Anyway, I don't know why "Lisbon" can be a target of a crusade. Maybe the % of heretics/pagans/whatever is high and therefore there is any mechanism which allows it, I don't know. If someone can give any kind of feedback it would be very appreciated.
Regards.
Edit: I realized why Lisbon and others can be a target although they are not inluded in descr_regions. New settlements can be added if their factions are excommunicated.