I think that it might be a nice idea to use an innocent bystander rule here. For every round fired that misses it's target. Roll a D10. On a 1 you hit a biological being, servitor, xenos or human and do normal damage. On a 10 you hit something you wish you had not hit. Like power cables, plasma vents, steam pipe, a holy icon etc. If the weapon is powerful enough you kill the being or damage the component.
The results, that while on the macro scale of things probably does not count, can make the local enviroment troublesome. Exploding tanks for example could count as exploding like a frag grenade. A rupture in a plasma conduit could send out bolts of like a plasma gun that fire randomly. Killing your own crew will have a negative effect on morale if done often enough and could jeopardize the proper functioning of the component the firefight is taking place in.