Not sure if combat transporters is a bug or what, but you will not get pass a good missile base and of course if they have barrier shields no ground troops can pass them.
They will get by to some degree if they have only fair defenses.
The AI will surely blast down missile bases if it have good tech, otherwise it won't. What do you have for planetary defenses? Planetary shields can stop some things, so if is a function of you tech vs theirs.
I have them attack my MB, even when they fail.
Also the level has some impact, I am talking about at impossible only.