How do missiles work?

I'm trying to understand how missiles work. I've been wrecked multiple times in my game where I have a stack of units (eg 5 super tanks, 10 infantry) aboard a transport that gets attacked by a missile. Every time the transport survives and all the units die. When I try to attack any enemy's stack of bombers, for example, only 1 of the bombers is killed. Am I losing because my units are on a boat or air transport? If so, why are the transports surviving and all the other units are dying? If I had a stack of missiles, would they all die if attacked by one bomber?

What map are you playing? We need to know the stats of the missiles, bombers, and air transports in question.

Can you provide some screenshots and more info.