Often I have had this problem. like mrxak said, it is usually becuase of the range of the weapon. Other problems howeveer, are that there are other weapons on that ship too, and so does no allways use the particular weapon you intend for it to primarily use, or the AI ship type was set to something like wimpy trade, whereas it rarely ever fires. My wimpy trader I accidently created had 300 nanites, tons of FPT, and disabling IR missiles. The ship was a polaris Arachnid. When it was fired at, it simply ran off, and went into hyperspace. Check these, then try again.
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