crossbows have a few issues, but basically its that a few haulers or goblin recuits with wooden crossbows and cat bone bolts can stand around mangling brains and sometimes punch right through steel plate and instakill things from half a screen away.
The big one is the 2 critical boost (for the bolts) that you can't just go and decrease in the raws***. Each attack gets to roll some dice or something for a chance at becoming a critical hit. Critical boost 2 means that our little bolts get to try them again 2 extra times, which sounds like the reason they sometimes go and mangle 2 lungs and a heart at the same time. There is alot more to it then that but only Toady really knows how all that under the hood stuff works.
Also, Submachinebows. Lots of marksdwarves each shooting lots of bolts that each have lots of critical boost = (lots)^3 of dead stuff. With agility and training crossbows users basically switch into full auto mode and just unload bolts for the second or two the ammo lasts.
Also, Crossbows also have range and first strike and economic and strategic issues, which are hugely important for a dorf fortress. Crossbows are cheap, reasonably effective even at low skill, exponentially effective in large numbers and with a champion or two in front nothing gets close enough to fight back. Remember, goblin/etc life is cheap and plentiful, if a whole siege is slaughtered but they kill your armorsmith or farmer or that peasant everyone is friends with, then the goblins won that siege (or its a tie maybe).
anyway I have been working on nerfing ranged weapons for the past few forts with surprisingly good results.
***creatures and their organs are highly moddable
To nerf crossbows, I went into the raws and removed:
[circulatory] from hearts
[throat] or something like that from throats or necks or whatever
[nervous] from spine, brain, neck (spine+neck seem to be sparring/wrestling things, but taking nervous off of brain seems to drastically reduce bolt instakills)
[guts] from guts, although this doesn't seem to effect crossbows much, I think its a sword critical
And then added:
[sight] to brain, mostly as a backup but you could probly mod out eyes then since at this point all they do is get shot out anyway.
And then you need to add at least two more lungs (by just copypasting the left and right lung and then naming them left lung 2, 3, etc) because individual bolts can take out 3 lungs at a time, and they often will because there isn't much else to hit anymore. I have a woodcutter walking around who cancels his jobs and passes out every once and a while because he lost 3 of his 8 lungs, so its not perfect but he gets along fine and only has like 2 toughness anyway. Now that I think about it, just giving dwarves and everything you fight [nobreathe] might work much better, but that has some side effects.