Military doesn't like me capping pirates?

[Rapsey]

I've just completed a simple "Defend the station" mission, and quite successfully too! Three pirates ejected, so I claimed their ships.

First, I claim a Hades. Almost immediately I hear the combat music, yet there is no enemy contact on sensors. After about 30 seconds the Hades blows up. Message log indicates it was destroyed by a Paranid Military Deimos.

...okay, I guess. I take the second ship (a Buster Hauler) and the third one (a Falcon). This time it takes a few minutes. I was almost done reparing the Falcon when.. yep, combat music! This time I see an enemy Boron Heavy Hydra coming my way, apparently it had launched a missile at the Falcon. I decide to fight back and immediately half the sector turns red.

I'm in good standing with both the Paranid and the Boron, so why the sudden aggression against these two newly capped pirate vessels? Is this a bug, or do they have a reason for blasting my ships into oblivion?

EDIT: This took place in Trinity Sanctum.

[Coreblimey]

This is one of those little nuances of the game I'm afraid! It appears that the three ships concerned were already targeted as enemy by the Paranid & Boron vessels. Although you capped them and are now your property, those to ships don't agree! They are still enemy targets. Hence KABOOM! It is also that they were destroyed by missiles already fired. (Well in the Hades case anyway.)

[Nanook]

More likely, especially in the case of the Hades, one or more missiles had already targeted it, hence the almost immediate combat music. I'm betting that the Hydra had also sent missiles at the other ships, resulting in them being shown as enemies as soon as you took possession. Sometimes the NPC's just get in the way of profitsssss.

[Rapsey]

Oh great, thanks.

Would docking capped ships ASAP prevent this kind of thing from happening? (Unless the missile is already underway of course.)

Also, would the military consider it an offence if I shoot down their long range missiles? I think I'm gonna have some fun experimenting with this..

[Nanook]

Oh great, thanks.

Would docking capped ships ASAP prevent this kind of thing from happening? (Unless the missile is already underway of course.)

Yes. And the missile(s) will lose contact as soon as you do, so you'll be safe from them, too. Experienced players often bring a TM or other ship capable of docking fighters to the party, and dock any captures immediately. Jumpdrives are handy for ships that can't dock in other ships, too. Just transfer one to the captured ship, along with some energy cells, and have it jump away.

Also, would the military consider it an offence if I shoot down their long range missiles? I think I'm gonna have some fun experimenting with this..

You can shoot down missiles with no affect on your reputation.

[IceDown]

I'm not sure if docking will help, but there shouldn't be a problem shooting their missiles. Missiles don't belong to anyone like ships do. If the NPC still thinks the ship is hostile, as soon as they are destroyed, it will launch more.