Colony Model gives building not only from era 1 and 2, but from era 3 too. So, when every new city is created, it has all medieval buildings, which player can build.

Another thing. Technically, it is not a bug, but serious balance issue. When discovering Feudalism, no city in all world has all building in it, but every new city do. Seems, this mechanic needs to be changed. For instance, Colony Model should give access to 10 owner chosen free building from from first two era, but not 30. Or all building from era 1 in medieval era and era 1 and 2 in industrial era (it is easier to implement).