NEO: What vase? [Turns around to look for the vase and breaks it].
ORACLE: That vase.
ORACLE: What's really going to bake your noodle later on is: would you still have broken it if I hadn't said anything.
Well, we'll never know, will we? The Oracle and Neo only exist in a universe where the Oracle says this and Neo breaks the vase. The Oracle knew this would happen but doesn't know what would have happened otherwise, because she knew she would always say that to Neo. This quote not only brings into question Neo's free will, but the Oracle's as well.
ORACLE: As soon as you step outside that door. You'll start feeling better. You'll remember you don't believe in any of this fate crap. You're in control of your own life, remember? Here, take a cookie. I promise by the time you're done eating it, you'll feel right as rain.
Oh the Oracle. She just can't help herself. She is prophesying Neo's future about how he's in control of his own life, completely subverting anything he was about to think about fate. How can he feel better after eating a cookie when she has told him he will feel better? Now that's all he'll be thinking about.
SMITH: You hear that, Mr. Anderson? That is the sound of inevitability. It is the sound of your death. Goodbye Mr. Anderson.
NEO: My name is Neo.
Good job Neo, you can say your name. You've officially made it out of preschool. Okay, maybe what Neo's saying is more than his name; he's finally accepted his identity as The One. He finally sees himself not as his residual self-image of the Matrix but his true person. Smith's quip about inevitability rings true because a train is a vehicle whose course does not alter. It follows the same tracks and these tracks lead toward Mr. Anderson's death. In a way, Smith is right. Mr. Anderson finally dies as Neo (very literally) rises.
MORPHEUS: Do you believe in fate, Neo?
MORPHEUS: Why not?
NEO: Because I don't like the idea that I'm not in control of my life.
Hmm, Neo's reasoning seems to fall into the wishful thinking fallacy. He doesn't believe in fate because he doesn't like, or agree with what believing in fate would imply. It's scary, really: thinking you're not in control of what happens to you. But just because it's scary doesn't mean it isn't the case. We don't like to believe that eating triple chocolate cake for every meal is unhealthy, but that doesn't mean that it isn't (not that that stops us…).
SMITH: I must get out of here. I must get free.
Up until this point, we assumed that, because Smith was a program, he was operating purely under the will of the machines that had programmed him. But now it appears he is autonomous. He has a mind and a will of his own. He is not happy with his station and will do anything to escape the "zoo" or "prison" of the Matrix. In one hand the movie questions whether anyone has free will and in the other it provides evidence that even a program, which simulates an agent in a virtual reality, can possess it.