For me infantry is often getting stuck and unavailable, mostly on contact with some fragments of buildings and ships.
Is it possible to implement some advanced controls of infantry? To make it group, stand at point, select it partially?
I've been getting this too, usually they'll get stuck on the very ship they've just fled.
I'm thinking it's a problem with their "go up first" pathing system.
I've lost quite a few marines to otherwise simple hijackings because they want to climb the balloon instead of jumping out the cargo door like they're supposed to.