[AreaOfEffect]

The computer doesn't always aim for the middle of squads, as proven by illithid mind blasts. Remember, spell casters and archers pick targets differently. Secondly, unless your squads were very far apart from each other, unlikely with that many troops, it is possible that many of the shots went wide enough to hit nearby squads. Lastly, crossbows have an accuracy of 2, which I assume moves the total precision to 6, not 4. Pardon me if you already accounted for this by the way.

One thing I like about well equipped units is that weapon bonuses apply as normal in darkness. Soldiers with shields and broadswords will still rock a lot of socks if the opponent isn't undead, a demon, or have darkvision. You might even be giving the opponent an edge if your not careful.