Originally Posted by M134

Never played this mod, but I've heard similar complaints in EM. In that cases players was intercepted by ASW patrols near target location. When you intercepted like this you're spawn in a mission area but this is NOT a mission. You can hit "Escape" and check if you actually have "Misiilie strike: 0/X" requirement. If not - do NOT fire your missilies, this will not count.
Dunno if it is your situation, but it could be...