User blog comment:Suparockr/List of Plotholes throughout the series/@comment-70.143.64.2-20120723023327

Real plot hole:

The Citadel: It's actually inhabited by the self described collective will of the Reapers.

Yet this collective will didn't interfere with the Protheans using the Conduit to arrive after the last apocalypse and sabotage the Keepers. It didn't activate the Citadel relay itself. Indeed, why would the keepers even be necessary for this? The Reapers also had to physically come and take the Citadel to Earth after TIM revealed it was the Crucible.

Thus the 'starchild' has no power whatsoever, or even connection to the Reapers, since it could have shared knowledge of the Prothean plot. Yet it's supposed to be this powerful AI, the very embodiment of the Reapers.

There are no answers to this. After all, there wouldn't have been the whole Retake thing if the Citadel Reaper AI fit into the story.