The humans have been hearing rumors of something out there that's new to them. But it's not hard to believe that they think that anyone with the military presence to wipe out a Narn fleet is something they would have heard about well before now.
Part of this whole arc is them slowly coming to the realization that there's a force out there that is a match for Vorlons that they didn't have a clue about.
It'd be the same if race of mole men that live 100s of miles below the surface eliminated the dinosaurs, and have just been biding time for millions of years. It's not going to be our first thought, because we'd assume anyone that powerful would have been active.