Visible crew/equipment: As the Oracle stands up from the bench, right at the end (after she says "Someday"), you can see a strip of yellow tape on the back of the bench marking the right place for her to sit. (01:54:40)
Continuity mistake: In the scene where Neo sees the oracle at her home, as the shots go back and forth during the dialog immediately after she sits down, her cigarette pack goes from closed to slightly open several times, until she takes a cigarette, then it stays slightly open. (00:25:00)
Revealing mistake: When Smith goes to see the Oracle and he puts two of his fingers inside her forearm, if you pay attention, there is a circle where the green effects start, they don't start from inside. (00:33:25)
Revealing mistake: During the battle of the dock, just before Shara takes her second shot at the digger, she is seen from behind as her weapon is being loaded. As Zee is about to slide the rocket in, the green screen is momentarily visible through the barrel. (01:05:35)
Continuity mistake: In the scene where Bane has the scalpel to Trinity's neck, the bloody mark below it keeps disappearing and reappearing. The scalpel changes positions too as well as the blade itself changes. (00:52:55)
Continuity mistake: When Trinity is meeting with the Frenchman, the olive in his martini changes. In the first close-up shot, he only has one green olive on the cocktail stick. From then on he has two, until he eats one. (00:19:50)
Revealing mistake: In the subway scene, when Neo gets slammed towards the wall (and crashes into it) it's visibly Keanu's stunt double.
Revealing mistake: When Neo and Smith are fighting at the end of the film - when Smith knocks Neo into the rafters of the room they are in, you can see Neo's face, and it's obviously Keanu Reeve's stunt double. (01:44:30)
Visible crew/equipment: When Smith and Neo are fighting in the building Smith is knocked to the floor. When he gets up you can see the stage light in his glasses. (01:44:35)
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