The parallel routes are only not playable with 2 or 3 players. With 5, you should be able to use them both ( although not by the same player). I've never had an issue with the iOS version. Are you sure it's not letting you use the second route?Well, the rulebook calls them "double routes", and defines "parallel routes" as a route that goes from A to B, another that goes from A to C, but from A and a bit down, they look like they both go to the same city.
I don't know why, but they devoted a whole block + illustration just to cover that.
As for the topic, yeah, double check to make sure you indeed can't build (e.g. you're not tapping it correctly, or you do not have the appropriate train cards)