Agent smiths differ from the other Agents

[Agent Pace]

I'm not sure... The One's purpose was supposed to end at the Source. It is stated several time, the purpose of the one was to save a handful of people to rebuild Zion, and sacrifice the rest. The Architect isn't able to predict something that doesn't go with logic, so I doubt this eventuality was anticipated by him.

As said before, maybe the Oracle did it, but I don't know... I always figured she influenced stuff with prediction, not creating rogue Agents. Truth is, we may never know.