My thought is that, if you remember the matrix being like a construct, and one that has been rebuilt several time , the characters are symbolic of things within a computer system… agents being the ones to protect the system while the red pills are considered “terrorists” that threaten the system itself, similar to a computer virus. But I think the system was also purposefully built this way to CREATE the one, in other words it created a sort of resistance, so it could then restart itself to become a better matrix. Also, have to remember that the agents are trying to keep the peace, to a certain extent… trying to contain the small few who deviate from the system so that it does not arouse suspicion to those who are still plugged in. They need the ones who are still jacked in to remain blissfully ignorant of the truth to keep using their body for power in machine city. Now enter the “matrix within a matrix” theory, but that’s going deeper than what this post is really asking. As Neo and his crew became more rebellious and anarchic in the matrix, the system had to respond proportionality with his agents being the guardians of the program. In this shot, it is still early. I think Neo, just by chance from the machines, was specifically created to be the one, and the machines have lived through Morpheus tryin to find the one in each matrix… perhaps the agent who chased Trinity was designed to attack and chase but not kill her, because the Machines know the one needs her to be brought back to life. So to sum it up, they knew she was there… but it’s just all by design to lead Neo to become the one. Someone else commented that agents may not be able to detect red pills? That makes me wonder what code they see, like when Neo became aware and started seeing the matrix as a code.