As mentioned in the Misc Modding Questions thread, I was having issue getting AI controlled ships to use their missiles effectively. I have just been able to replicate the issue on a clean install (barring console commands):
Fleet Doctrine: Reckless
Skills: [Weapon Drills, Coordinated Maneuvers, Crew Training], [Navigation, Gunner Implants, Electronic Warfare, Flux Regulation, Automated Ships]
Ship: Guardian
Loadout: Large Composite Hardpoints - Hammer Barrage, Medium Missile Hardpoints - Annihilator Rocket Pods
Weapon Groups: All on the same group, firing mode set to linked.
Sim Opponent: SIM Quirinus; Dominator, Heavy Rocket Cruiser
What happens is thus:
The Guardian fires an opening salvo of missiles.
~10 seconds later, the Guardian fires another single salvo.
~49 seconds later, the Guardian fires a third salvo.
~ 9 seconds later, the Guardian fires a final salvo of missiles.
The Guardian then never fires another shot, the enemy eventually dying to CP depletion (over 8 minutes after the last missile was fired).
During all this, the Guardian's weapons never go offline, nor does the Dominator ever escape weapon range.
Update: Removing the Hammer Barrages fixes it, as seemingly does setting auto-fire to Alternate. Removing the Annihilator Pods (leaving only the Barrages) exemplifies the issue, with the Guardian firing once on approach and then maybe once every couple of minutes.