Are you sure? There's code specifically to abort the inspection if the player jumps out before they get the notification about the scan, and as far as I can see, it seems to work. Can you describe exactly the sequence of events?
Yes, I'm positive of what I saw.
I was near a Hegemony patrol when I arrived at the warp thingy, clicked the text option to enter warp, and afterwards while my fleet was just kind of fading out while on top of the gate, the hegemony patrol emitted its pinging pulse thing, and then I appeared in warp in time to see the "you lost faction!" message.
I also recently chased down a single pirate ship, some kind of smuggler, engaged it, used the "pursue" option, ran it down, destroyed it, and when I came out of combat I saw a notice of losing -156 faction with independents, and since the game was paused, I got to see that the now empty pirate fleet (of one ship) I had just killed had turned independent after I engaged it.