Given the way one of the crews came back mad with fear...
How about the Advent, there's nothing saying that they didn't end up in vassari space when thrown out. The Advent even turned up after the Vassari in TEC space so it would kind of make sense from that PoV.
Alternativly, what about them conquering a world, unaware that it had a native popul;ation living, (for some reason), underground, which then silently built up their forces and spread themselves across the empire before striking. No need for fancy phase space stuff if they're allready everywhere, (would make for a cool extra faction too, i have a fair few idea's vis a vis this here). You can't defend against an enemy thats spent decades/centuries/whatever studying your weaknesses and secreting themselves on all your worlds via trade ship to rise up in one huge burst, overwhelming you.