A Muton always comes with a 6-piece armor (except for the very first one you encounter). They have a small 6 part armor icon next to their health bar which looks like this...
If you have a Support in your team you can have him use Weaken. That'll take care of quite some armor.
Just make sure that every part of it is grey before killing the Muton. If there is only the slightest bit of armor left when you finish him off it won't count towards the Trophy. Simply double check before you land the final blow.