Having just a moment ago slain one of my prisoners, I find that I'm unable to retrieve his ear because he won't show up on my scanners, despite having been executed on an open street in broad daylight. I can see his "unconscious" body from my cockpit, but when I exit the ship to get the trophy, like it says I can from my cockpit but refuses to, he's nowhere to be found.

Eh, a case of his stealth being greater than your perception, even though he's dead. I'd bug base it.

Nicolas is correct, if you can see the body from your ship, but cannot do so with your own perception, then it is a matter of stealth.

I'm not sure if bug basing it will change much though, in all honesty. Stealth isn't an "ability", it's not something that can be cut on or off, it's more of a natural feature. Someone has a certain stealth status, if they want it or not. Defels cannot be seen even by their friends in the open if those friends are not in their faction, unless their friend's perception skill is high enough.

Bug basing it certainly is a good idea, but I wouldn't be surprised if nothing will be done about it.

Skills should not apply once you are dead. It shouldn't be hard to fix, one way or another. Perhaps simply render all skills to 0 on death would be simplest. Or a more directed fix of editing the way scanning works to ignore stealth if the target is dead, but that wouldn't help if this starts happening with more skills, for whatever reason.

Stealth is not an ability? I disagree with whole my heart. Natural feature of being transparent, shadowy or whatever is only a part of stealth skill, and even then only for a very few sentient races. What I believe stealth describes mainly is the ability to sneak and hide, using both your agility, know-how, inherent agility or other helpful race-related feats, like the Defel one for example. And you can't exactly sneak, use the best of your knowledge and agility to hide or camouflage yourself, when you're dead. A dead body only hides as well as the terrain it fell into does.