Like 3/4 of the battles I fight one of my characters cannot use his missile weapon. I have two characters with missile weapons, and one of them can always use it and the other almost never is able to. I can select the use missile command on him, but every enemy gets a no symbol when trying to use it. The other character is always able to use her bow though. There seems to be line of sight as well...

Any idea why this is happening?

I haven't played Darklands in ages, so I'm not quite sure which of these applies here. In any case, I'd check for range, especially if your character wields a thrown weapon or shortbow.
Check if your character has ammo and that it is the right type of ammo.

I didn't realize that your party itself could block LOS to a target. Problem solved.