You might also be experiencing a problem with not having the right strategy in Auto/strategic combat. Some of the strats don't target missiles, or even fighters. You may have to choose or make a different strat that will take care of the treat. In CB it is the use of specialized ships to fill specific roles.
You can go here and find out more about CB mod.
http://imagemodserver.mine.nu/other/...CBmodTutorial/