A particular Dominator variant really doesn't want to fire its Hellbore cannon or its other forward gun (Heavy autocannon). This is usually happening when the enemy is overloaded, but not always. Another observation that seems a bug: The ship never puts its forward hardpoints onto autofire, ever, so it won't fire its two main guns at the same time or keep up fire with either when its 'thinking' about firing missiles.
I don't think this is a mod issue, as this is in the simulator and the variant I'm using has only normal weapons, but I do have three mods enabled: Nexerelin, Ship and Weapon Pack, and Lazylib.
This is the variant. Weapon groups are the default auto groups, except that the Reapers have been set to linked. (Groups can also be seen in the combat pictures below). Officer is Steady with missile spec 3, evasive action 3, and impact mitigation 2.
This is in the simulator against the Outdated Enforcer, where I got it to reproduce most of the time. The Enforcer is overloaded but the only weapon group active is number 4, so the ship is firing a single railgun instead of either of its forward guns. It has no flux built up and max dissipation. At first I thought it might be concerned about missing because of the maneuverability of the target and the slow shot speeds, but thats not the case below.
The image shows the Dominator going after a Punisher (Ship and Weapon Pack) in the simulator which is overloaded. The same situation as before, only now it is definitely going to hit if it fires the Hellbore.
[Edit] I just split up the hardpoints (heavy mortars) on a Balanced Hammerhead into two seperate groups and they show the same issue: they never are put on autofire, so they never fire at the same time or when the ship is thinking about its missiles.
[Double Edit] Actually, looking at my screenshots above, in both cases the Dominator has its Reaper group active like its "thinking" about firing missiles but it doesn't. This combined with the "no hardpoints on autofire" might be whats causing it to just not fire at the target? Because the target is overloaded it thinks its vulnerable to missiles, but then doesn't fire because of the target's maneuverability? I've sometimes noticed that the Dominator will "snap out of it" right as the target finishes its overload and puts up its shields - the missiles are not longer hogging the active fire group?