To add to what Spyder said, also make sure your AI Commander has the vehicle faction set in the force faction line. So for instance, this would be done in a situation where you placed a helicopter down from a faction different than the one you're using or when the faction name for the vehicle itself is different than the other units. Example, 3CB Units use a different faction name for their vehicles so I need to have the infantry faction name and the vehicle faction name in the AI Commander module. This is unusual but it's worth pointing out.
If I don't do this, they act exactly as you described.