You mostlikly miss a torpedo.
Start your QB with yourself as the borg ship and a couple of asteroids (or small, weaponless, stations, such as the communication array).
Next, test out each torpedo and pulse weapon on the ship one by one (start with the torpedoes, since you can easily test each on itself).
Mostlikly (from the description you have given) it's a missing torpedo file.
Note how many times you had to click for the torpedo if it crashes.
When you find the problem, open the torpedo property of the hardpoint and find the correct torpedo in it (you will notice the link between the number of clicks and the torpedo entry).
Or, if you don't know about hardpoints, contact the author for a fix, and make sure you have read the readme correctly for any dependancies (such as projectile packs).