Since Entrenchment, I've had missiles as a fighter-to-fighter weapon in a mod. Recently, I have noticed that having missiles projectiles on a fighter means that they will act as bombers, and will not target enemy fighters, this occurred due to a minor change in the ANTILIGHT attack type.
To explain, the reasoning was that, as the AttackType had a higher damage modifier versus Pirate armor than VeryLight armor (ex. 1.01 vs. 1.00), the fighter acted as if it was a bomber, and refused to attack fighters. This oddity regarding Pirate armor also applies to all other armor types, with the exception of Medium armor (ex. you can have a 1.3333 modifier versus VeryLight armor, and a 2.0 one for Medium armor, and the fighter will function normally).