Mylian Troops are military/militia people fighting for independence from Amestris. Despite not being 'evil', they have prejudice against anyone from the nation and will attempt to kill them.
Milos was once an independent nation from Amestris, and rivaled its power. After King Bradley began the expansion of Amestris, they absorbed the nation. Milos dreaded this, and fought for independence, often harming innocent people as a result.