All redpills have Machine implants, so they can be hooked into the Matrix. The One's programing allowed him to broadcast to the sentinels outside the Matrix. (Nice wireless setup, Neo!)
Illyria
first of all, the sentinals are the "grunts" of the machine city, being that, they have a combat system with strategies, and tactics, however not a true AI
the sentinals are controlled remotely
the way the pods work is the machines developed the pods to contain and keep the humans inside asleep, unaware of the real world, the human body does not contain the hardware to interact directly with a synthetic interface
so the machines developed a way of physically connecting a human upto "the system" however wires alone does not connect a human the system, so something was needed to bridge the gap between the organic and synthetic, nano-machines were created to translate between the organic and synthetic
so as others have said, neo used his connection to the sentinals to make them stop, it was not a flaw in the nano-bots of neo, it was a flaw in the sentinals, they were far from their remote control source, and neo's nano-bots signal was greater than the machines
so when neo went to the machine city, the signal he sent out was quickly overwelmed by the signals from the machine city
first of all, the sentinals are the "grunts" of the machine city, being that, they have a combat system with strategies, and tactics, however not a true AIthe sentinals are controlled remotely the way the pods work is the machines developed the pods to contain and keep the humans inside asleep, unaware of the real world, the human body does not contain the hardware to interact directly with a synthetic interfaceso the machines developed a way of physically connecting a human upto "the system" however wires alone does not connect a human the system, so something was needed to bridge the gap between the organic and synthetic, nano-machines were created to translate between the organic and synthetic so as others have said, neo used his connection to the sentinals to make them stop, it was not a flaw in the nano-bots of neo, it was a flaw in the sentinals, they were far from their remote control source, and neo's nano-bots signal was greater than the machines so when neo went to the machine city, the signal he sent out was quickly overwelmed by the signals from the machine city
Um, Sentinels do have AI's. The commandos are the RSI representation of the sentinels that were sent to attack Zion in the third movie. Further more, in the animatrix short, matriculated, the humans make an effort to convert the AI's of the bots rather then reprogram them.
The pods arnt designed keep people locked up but to just hold a human body, feed them and harness the electrical energy of the body. If the pods were meant to hold a human against there will, Neo and all the other redpills would -never- have been able to wake up, with or without the redpill, and easyly pushed threw the gel skin that forms at the brim of the pod.
You have to remember that the machines base the matrix on the concept of choice and or the illusion that one has a choice. Most, if not all, that is done by the machines when it comes to humans is to maintain this idea and illusion including the use of sentinels and agents.
As for nano bots, that was talked about in the ultimate edition as a way the interface works, but I believe it was never confirmed as being THE way it works.