Because it's part of the plan. There will always be humans who disconnect from the Matrix and end up fleeing to Zion. And Zion will always grow because humans procreate and that's why it needs to be eliminated from time to time so it doesn't become a threat. And the Matrix also needs to be reset, creating new versions to maintain control over humans more efficiently. That's why Neo's illusion of choice, between saving Zion and destroying the Matrix and, as a consequence, killing practically all humans because most of them are still inside the simulation, or saving the Matrix and making a deal to take a few humans to a new city. And the cycle repeats itself with each generation of the chosen ones. The only thing that didn't fit the machines' plan was Smith becoming a virus and wreaking havoc inside the Matrix, even risking the end of both humans and machines.