I'm guessing that once the marines capture a ship, all of the enemy NPCs are removed just as it's about to switch over ownership to the player. In that short instance where the NPCs were gone, but the ship was still converting to my property, the despawn command must have been executed. I've seen this kind of behavior before when watching a ship being captured as it's turning (minus it jumping out xD). It'll kind of "snap" back into place the moment it converts into the player's property. Either because it's resetting the animation, or it just spawns a clone which is the actual ship you gain after the capture is successful. I'm sure someone who knows more about how this game works (Cycrow

Regardless, I suppose you can consider this a bit of an F.Y.I. for anybody considering capturing assassination targets.
EDIT: I actually recorded it happening, as I was trying to record a regular video at the time. https://www.youtube.com/watch?v=mzqunop3Ua0&t=3m59s
tl;dr If you plan to capture an assassination target with marines, I'd advise against it. The moment the marines capture it, a script that despawns the ship will execute. This will delete the ship, and all of your marines.