Giving a build command will stack air units and also build 1 per each Commando selected.
Selecting 2 Commando to build a transport will end in 2 stacked transports, with no visual confirmation that its 2 of em.
I dont think its suppose to work like this? I would rather see Commandos build air units the same as ground units. I guess this is a part of the air-stacking 'bug' where air units dont have collision(?) on ground so they end up in the same place.