I dont know how you people see that, but i guess depende on your grafic setup you dont always see your companions firing. Or you just dont see it because of the tension in fihts.
But, i find a lot of times people passing through friends when they are firing and then they get fired to with friendly.
Maybe doing boxes of companions bigger so you cant pass trhough directly but you have to turn around.
I dont know. The problem i see too often is people passing through others when they are firing. And when you are scoping, aiming, ussually you hit yoiur friends cause they are in front of you but you dont see it at all.