OP, just assume you're never alone in Res during a CG, even if you don't detect anybody at first. Probably the guy was silent running, but I still think it's possible you just missed his icon as you were in the middle of combat.
Last night I was at the CG and the Res was empty and I'd been there long enough to burn through all of my ammo. I had been battling a wing of highly ranked NPC's and my shields were gone and I was down to 60% hull as I destroyed the last of them. I was just getting ready to reboot the ship when all of a sudden I started taking fire. There were no more angry NPC's, and I was very confused. There was a cluster of NPC's on my radar all kind of knotted up close together and at first, I couldn't make out the red enemy warning, then it kind of cleared up as I moved away and I saw that I was taking fire from a CMDR. I was flying FA Off so I retracted my guns and just started boosting away, 4 pips to ENG. For every boost I inputted a random direction including spiraling madly through the asteroid field. I zigged behind, over, around and under every rock I could get to, the entire time with this guy whittling away at my hull and FSD. He chased me for about 4 minutes before I was able to get enough distance to scamper from the cover of the Res, clear the masslock and high tail it to the station to repair and rearm.
So, moral of my story was pay more attention I guess. And when you're attacked, as it is inevitable that you will be at some point, if you can't fight run like hell using any object you can to give you cover and a chance to escape.
With all that said, it's stuff like that that I live for in ED, that white knuckle kick of adrenaline that NPC's just can't give you. That story (and the part where I rearmed/repaired and went right back and found him in SC a minute later) was the highlight of my evening, and the main reason I even go to CG's in the first place. My advice is to send the guy a friend request and keep an eye on his marker and then go destroy him some day soon when he least expects it