You need to specify that "city" means metro area. Some of these, like Getafe, are named after the cities they're in, just cities that aren't the focal point of their metro area.
Getafe is actually the name of the CITY where the club is from, it's a different municipality from Madrid. It's especially surprising that you don't consider it a different city when the answer for Olympiacos is Piraeus and not Athens, because it's the exact same situation.