Why are such anomalies generated?

The first Matrix was mathematically perfect, and there was no anomaly; however, in such a world, human beings were not able to accept the reality and refused it. This is also mentioned in THE MATRIX by Agent Smith.

Agent Smith: Have you ever stood and stared at it, marveled at it's beauty, it's genius? Billions of people just living out their lives, oblivious. Did you know that the first Matrix was designed to be a perfect human world. Where none suffered. Where everyone would be happy. It was a disaster. No one would accept the program.Entire crops were lost. Some believed that we lacked the programming language to describe your perfect world. But I believe that as a species, human beings define their reality through misery and suffering. The perfect world would dream that your primitive cerebrum kept trying to wake up from. Which is why the Matrix was redesigned to this, the peak of your civilization. I say your civilization because as soon as we started thinking for you it really became our civilization which is of course what this is all about. Evolution, Morpheus, evolution, like the dinosaur. Look out that window. You had your time. The future is our world, Morpheus. The future is our time.

Because of this, the Architect redesigned it, considering human imperfection. Then, when he was frustrated by troubles, one program found the answer of giving humans the right of choice. Due to the concept of choice, almost all people could receive the reality. To tell the truth, it was the Oracle who found it. She was orifinally the program to investigate certain aspects of the human mind, so she understood humans better than the Architect.


What does the One exist for?

The function of the One is to go to the source of the main computer and reload it by reinserting the code he carries. Then, he selects 16 female and 7 male to rebuild Zion.
That is to say, most people in Zion die by reloading the Matrix. Unless the One reload it, human beings are annihilated by the system crash, on the other hand, if the One fulfills his role, most humans are ironically to die.


How is Neo different from the other predecessors?

As mentined before, there were five predecessors before Neo, which means that they five chose to go to the source and reload The Matrix. As a result, Zion had been rebuilt five times. In contrast, Neo chooses to go back to the Matrix in order to save Trinity from Agent. That is, specific love toward one person rather than entire humans is so strong that Neo chooses another way different from other fives; consequently, his action becomes the new step for coexistence of humans and machine which means the war is over. Neo is an anomaly of anomalies!!