Continuity mistake: When the "Hammer" is being chased by the sentinels we have one shot of its captain in which he says:"Lock that down". When he says this he has some type of earphones, but in the next shot he doesn't has them any more. Between both shots the ship doesn't make any move that could make those earphones fall nor time for the captain to remove them.
Factual error: The flight of the Hammer is a very bumpy one and more than once the ship is either upside down, on its side or straight up and down. The crew of the Hammer are completely unaffected by this and keep feeding ammunition to the guns. The Hammer's movements should be tossing them around since they aren't strapped to a chair like the pilots and the gunners are.
Visible crew/equipment: When Neo wakes up in the train station, Sati's dad tells her to, "Leave the poor man in peace." When she runs off, a piece of tape is visible at her feet, showing her where to stand. This is visible in many wide shots, but particularly in this shot.
Continuity mistake: In the final fight between Neo and Smith, when Smith throws Neo inside a building, he flies inside the building through the hole. When Smith is inside, his flight causes a lot of dust. In subsequent shots, the dust has settled in only a few seconds.
Answer: Neo was the One. Prophecy is not always 100% correct on all the details. And he did destroy the illusion of the Matrix and granted freedom to those who desired it. So he did end up fulfilling the prophecy in a way. It's much like Anakin Skywalker bringing "balance to the force" by annhilating the Jedi and allowing a new order to spring forth. Not exactly what you would expect.
Grumpy Scot