If there is an empty vehicle within 50m of the waypoint, the waypoint will stay on the Commander ui and the group will first move to the waypoint, and then board the empty vehicle. Setting up load waypoints for the transport groups does not help nor do making the transport units subordinates/not subordinates. Note that if you make a get in waypoint for infantry grouped with a vehicle, the infantry will simply mount the grouped vehicle.
This issue makes commanding large scale missions were you have to move units over large distances, a pain in the ass. Since you can not have a chopper stand by at your base and then call it in to pickup the groups. It also limits the players choices as a commander, and removes freedom from the player.