just got back from seeing it again...here is my thoughts
agent smith became an anomoly due to his HATE for neo. he went above and beyond an agents job description so to speak. thats my thoughts on him. so he transcended what he was "supposed to do" and rewrote his code as neo is able to manipulate things within the matrix.
neo's awareness of the matrix seems to stem from the possibility of it being another control measure within the matrix. one for people who wont accept the matrix as it is. i think.
here is what i have a feeling happened. neo's predecessors were forced to choose between saving trinity or zion. they always chose zion. greater good type thing. this time the architect knew that neo would choose trinity because the neo "anomoly" learned to LOVE. agent smith became an anomoly because he learned to HATE. the systemic anomoly that is spreading problems throughout the matrix is the fact that control programs are having human emotions evoked into them. love and hate. and since this has happened, the programmed rise and fall of humanity which has been looping is set to stop due to a falter in the program loop. this threatens the matrix and its control because all of the people would probably wake up. im thinking that there is minimal security in the "real world" to keep people from just walking out of their goo and pods and starting life on earth again. basically just a program that keeps looping to keep them complacent. a computer that wont die due to a continual power source of people, but downsized its security forces long ago due to the perceived perfect control of the matrix. hundreds of years had passed since humanity was enslaved, so why keep tons of sentinals for no perceived threat?
these are just my thoughts....based on how my overactive imagination works...hehehe. could be something in there....i dont know.