Take a look at this route:
http://goo.gl/maps/OO3nYou can compare this with a Directions Request in the Maps API. You gave three waypoints, namely A, B and C. On the map, every of these waypoints has a marker shown. This is because these points are all stopovers. If the stopover property for point B would be false, then the route would look exactly the same, _but_ there would be no marker where point B is (and in the directions listing there would be no visible break of the route).