How was it possible for Agent Smith to copy some abilities of Neo?
He thought in the first Matrix, that he killed him, but Neo woke up and killed Agent Smith.
And he used this technique like Agent Smith, Neo cloned himself into Agent Smith
But if he cloned himself into Agent Smith, there should be 2 Neos, but there aren't.
So there is one possibility, that this cloning caused an error in the Matrix and so Agent Smith was copied into the Matrix structure and was deconnected.
That's a strange structure, because there are programs in the Matrix, viruses (like the albino brothers), and the "PEOPLE" and the people who aren't in the Matrix and want to free the others.....
I think there a connection between the Matrix Architect (who is a program) and the Oracle (who is a program too).....