Friendly fire can happen along any point of the missile trajectory, since missiles are not just calculated kills, but have actual flight paths. It is very likely to happen if you run your unit through a missile unit while they are firing. The game calculates whether the projectile will hit anything very soon after the release, and if the answer is yes, that man won't fire (that's why fewer men will fire in the woods). However, if men are moving in front of or through the missile unit, the calculation may occur before they actually get into the "killzone", and therefore the projectile is released and your men buy it. Furthermore, due to their flat trajectories, xbows and arbs are more likely to cause friendly fire in general.