I thikn you gotta send troopers in, to do this:
select a team of stormtroopers, hold shift and right click on the bunker, then just plain left click on it to see if anyone's in it. WHATEVER YOU DO DO NOT SEND DELLIS in if you don't know what is in there. Bunkers give you more command points i think, but if it's a yellow bunker, i don't think yuou can take it over. sometimes you need to have the view far out in order to take over some buildings.