Complex sentence: Many were from state militia outfits which had their own state-issued uniforms, and in the early battles some Confederate units who wore dark blue uniforms were often mistaken on the field of battle for the enemy.
Split into simpler sentences: Many were from state militia outfits, which had their own state-issued uniforms. In the early battles, some Confederate units that wore dark blue uniforms were often mistaken on the field of battle for the enemy.