An enemy ace is simple a little tougher enemy and they start to show up a few missions in. such as Tanks. If you have the habit to kill everything in your way you can't miss this one. In fact you will have to try hard to avoid killing them if it's even possible to get through all missions without.
The achievement will now pop the first/next time you visit the command center in your headquarter. The last part is important to remember, because there isn't really a need to go here after you picked out your squad the first time and didn't meet the requirement at that time.