User blog comment:Suparockr/List of Plotholes throughout the series/@comment-1679409-20120717153223/@comment-4953843-20120717165544

vendetta already addressed it.

"its presence is inferred, rather than observed".

meaning the catalyst deliberately does not interfere until game-changing circumstances (e.g. completion and deployment of the crucible) force it to do so.

it didn't consider the keeper reprogramming as game-changing enough because there were still many, many avenues toward initiating the reaper holocaust.

indoctrinated saren -not- fiddling with the citadel controls when he still had spectre influence and authority, though....