Missiles and i assume fighters are not considered hostile when launched by a hostile enemy. For instance a scruple that shoots my drones will be fired upon by my drones, but a missile it fires will not be because it hasnt made an aggressive action against the drone yet.

This is very annoying. AI will select and target my gunners missiles with very rapid and great precision but slaves and drones don't know how to do the same. Have you tried aggroing your drones in that situation?

aggroing will indeed make drones shoot at anything passing by including missiles, but that doesnt resolve the underlying bug.

its the reason why my FC is so hard to kill drops. I have to sit 2k out with a RoP waiting for missiles to launch while the slaves kill the drop