It's important to note that the Matrix isn't actually that convincing a simulation of reality. It glitches regularly, the physics is weird, it requires periodic rebooting (including regular brain-wipes for the occupants) and is, for those that are aware that they're inside a simulation, immediately apparent to be a fake. In short, people are prone to noticing that they're in a sim and keep trying to find ways to get out of it, initially on a subconscious level, but eventually by actively trying to subvert the Matrix and find ways out. As Smith says,
... The perfect world was a dream that your primitive cerebrum kept trying
to wake up from.
The problem, as defined by the Architect is that all the glitches in the Matrix eventually become so apparent to the subject that they eventually realise, on a conscious level, that they're in unreality and reject the system. They end up mad, dead, suicidal or actively trying to subvert the system and eventually tell more people that the system is fake which creates a cascade of problems.
The Oracle came up with a solution, namely the Choice (with a big c). If people are periodically polled on a subconscious level to see whether they're happy with their reality, even despite the fact that it's obviously a dud, the vast majority will accept their reality. Conversely, a small number will choose otherwise and they can be safely ejected from the program and subsequently murdered.