Yep, missiles can be a real problem, especially if one of your enemies launches one in close proximity. -_-

Well, here's the thing that usually works for me. Do not launch your CM right after you get the missile alert. Wait a second or two, then press E and fly evasive maneuvers. If the CM didn't work, you can try launching more CMs. There is a certain probability that the CM will work, but that also means that you can have a streak of CMs simply not working.

Let me guess, BTW: are you, by any chance, currently at that mission where you're supposed to take pictures of a base on a planet's surface, flying solo?

When you hear the alarm, immediately hit afterburners and drop one decoy and turn sharply. Then look at the radar and maneuver to put the yellow dot (the missile) perpendicular to your flight path. Then if the first decoy doesn't work, drop another one after 1 sec... until it works. Or, if the missile is in view and not headed directly at you, try keeping it in view and track the missile instead.

Putting the missile perpendicular to your flight path is a real world technique called beaming. In WC3/4 you almost never get hit if you beam the missile properly, without using decoys.

Now the real threat is a) if the missile is fired at your tail real close and b) there are just too many missiles that you can't beam every one of them. To avoid a, make sure no enemy sits on your tail too close for too long, which requires good situational awareness. Good SA also helps you pick a better direction for the initial turn.

I just hit E a few times until the alarm stops! They give you plenty of decoys, and I've never run out.