theres another possible reason, alot of people have raised the issue that auto-cast on most abilities are pretty screwy, either the conditions for auto-cast or the abilites themselves.
so, for instance, a Kol Flak Burst will detonate when there are only 3 SC in range or something silly like that.
i guess its possible to program in some overriding rules like, IF any cap ship is below 50% hull, THEN auto-cast ability on said capital ship, rather than the carrier cruiser of HC or LF thats about to die, but i have no idea
maybe a fix will come out with the next update or X-pack