I'm having the same problem in my Venice campaign. I had two ballistas with my army invading Sicily, and fought several large battles with them. I had the ballistas on a hill in most battles, with my army deployed in front of them but lower down the hill. I found one of my ballistas obeyed my commands perfectly, but the other would only fire at specific units in the enemy army (usually the ones on the flanks for some reason). If I tried to tell it to fire at any other unit, the men would align the ballistas towards the target and then stand there doing nothing. Something I noticed that while they were stood there doing nothing, the little icon on their unit card denoted they were at "Firing" status.