Yea, there's lots of competing goals with the autotargeting. One of the things that won a DLC poll a while ago that we implemented was logic so that "if you only have overkill targets in range, go ahead and shoot them anyway", which is what you're seeing there:
1) The fort asked for a target list, got one, and the only thing actually in range was the bomber.
2) It processes the list, and the "oh, I've only got overkill stuff actually in range" logic kicks in and sets the fort's IsIntentionallyOverkilling flag.
3) It actually does the firing logic, and the IsIntentionallyOverkilling flag makes it suppress the usual "this thing is going to die, take it off the list" logic and it unloads the full clip on that poor bomber.
4) The fort asks for a new target list roughly every 2 game-seconds, but due to the throttles it's unlikely to get one immediately unless you don't have many ships asking for lists or they aren't having to search/sort lots of targets... anyway, it will wait 10 seconds before actually escalating the request to the higher priority throttle (or if it actually kills everything on the in-range list, it gets a different priority), so other stuff may come into range in the meantime, and the fort may or may not have them on its target list, and if it's not on the list, it don't get shot.
One thing I did add recently was another alternate-priority throttle for ships whose in-range lists are composed entirely of overkill targets (note that engine-damage-priority ships like spider turrets and Riot shotguns consider something overkill if it's engine-health-after-shots is less than or equal to the engine-damage-floor of the weapon), and that has helped a lot for some cases.
I guess, for irony and style points, I could add a control node for "don't intentionally overkill"
That wouldn't solve the problem outright but it would probably get the fort a new list faster once it cleared the list, and it wouldn't waste as much reload time (though a while ago we did change it so that "wasted" shots that don't even reach a target before it dies actually "refund" most of the reload time if it was recently shot, etc).
Anyway, I could go into more detail (there is actually quite a bit more), but I think that should do to demonstrate the complexity of the situation