That sounds like a problem with the collision detection. In smaller engagements, I've had warships friendly towards each other obliterate eachother with crossfire in both Open and retail. I believe 'friendly' beams are supposed to deal reduced damage, because I've gotten hit by small green beams and large vasudan beams and everything in between, and so long as the firing ship is friendly, it's painful, but survivable. Conversely, small green beams fired by hostile warships are pretty much instantly fatal. I'm not sure if the damage is supposed to be reduced for non-player friendly-fire victims.