Download the mission file, install the mission and load it up. Enter Commander mode using Ctrl+Space. Make a waypoint for one of the infantry groups (not the motorized infantry group or the chopper), right click the waypoint before the group reaches it and select Type->GET IN. The first infantry group will probably board the empty truck. If the first group entered the empty vehicle, it means you made the waypoint within 50m of the empty truck. In that case select the second infantry group and try to make them board something. Now you will notice the bug as described (if you haven't already). You can further test heli-extractions and vehicles grouped to infantry in the mission, if you want to.

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.