At this point you may be seeing a lot of issues with the two sides like happened early in the US Civil War where the Confederates were wearing US Army uniforms (taken in many cases from US Govt storehouses) - i.e. as in what happened at First Bull Run where a battery firing at the Confederates assumed the infantry unit coming up to them was supporting them - until they opened fired.
You could see the same thing here - a CivGov unit pulls into a town and sees troops there who welcome them with open arms - and then surround them and take them prisoner when they notice the unit insignia on the CivGov units and realize they are the "enemy" or vice versa - especially in places where both sides are in close proximity
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