I wouldn't be shocked; in my most recent game I had a protectorate claim FE sectors...twice. First time I wasn't ready (I wasn't expecting to start a FE/AE war until after I finished my Megastructure build campaign, so my fleets were underpowered for the time), the second I was. So now my protectorate owns a bunch of FE sectors/planets.I think there could be a case that AI does not respect FE somehow.
Maybe due to spying mechanic AI has no information about FE at all, and it does recognise FE as it, thinking it is another minor, and there is no code to remember this is FE.
As for the Khan, he's more a threat to the galaxy (which has very little understanding of this whole "build fleets" thing) rather then to you personally, provided you at least have some Battleships and a good system to defend in. But I generally start clearing out Marauder systems near me around that time just to prevent the headache.
Personally, the Khan (and frankly, the endgame crisis's) should spawn not based on year, but based on galaxy fleet power. You get more powerful early, the Khan wakes up early. Keeps the Khan more balanced relative to the player empire(s).
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