This is known, but I don't know if this can be 100% called a bug? It's actually a valid tactic, when pursuing an enemy ship, to fire missiles at it just to trigger its point defense. Even if the missiles don't connect, the ship will lose its zero-flux boost (but you won't if you had yours because missiles are generally flux-free!), so there's a tactical exploit that the player can use.
I agree, it's annoying to see on your own side. Maybe you're right, even in the above scenario the missiles are fairly likely to be a threat to the target, as opposed to completely missing. BUT then again, "PD-saturation" is a thing too! As in, there are types of weapons that excel at not necessarily hitting a target, but occupying its point defense so other friendly projectiles can get through - see Decoy Flares. So, while it's an odd thing to see a highly-advanced spaceship do, I think this calls for the [ Gameplay > Realism ] sticker.
If you really want to see such an AI improvement, I'd suggest putting it only in the obvious location: Integrated Point Defense AI, along with the function that lets PD ignore the aforementioned decoy flares.
