Arc Hyperion end game gigantic plot hole *spoilers*

Hm, similar to the way we sneaked to his ship when saving the Salarian ark?

As far as I could perceive, the Archon learned with every step taken, about everything he laid hands on. Nexus location was supposed to be unknown, rendering it temporarily protected from his sudden appearances (which wasn't the first time, given he traced and tracked us in hyperspace travel when going to Aya), but one he had that information from the Salarian Ark, he would attack the Nexus sooner or later. Knowing how SAM worked as well would give him an edge as not to make his presence really known until he had some control over the situation.

But that's just speculation. It might be then that the whole thing wasn't very well thought in the end.