Hi,
have you assigned the bus stop cube(s) to a specific track? If no, that's how it's done: You have already made a track for your line, so you have added tracks, there is no error shown, when you let OMSI check your track list. Ok, klick on "Add Station", then choose the track next to a bus stop cube in your track list (the chosen track turns yellow), klick on the cube and see if ou have a new bus stop in your bus stop list. Worked? Fine! go down your track list till you come to the track next to your next bus stop, klick on the cube and you should have two stops in your list. And so on. When you have finished your list of bus stops you can change profiles, make timetables. HAve fun!