[Imp]

It can be worth spliting the passengers from the vehicles, i.e. buy a Mech Company & delete the infantry, then buy the infantry as a seperate company. That way you can give the infantry if dismounted seperate waypoints to the vehicles.
This way you can send the infantry out on foot & control the vehicles seperatly though do note its very hard to get vehicles to follow infantry on foot if they get close enough they do tend to pick up passengers.
If you dont want this the simpliest work around is to adjust the carry capacity or load cost so it cant pick them up.