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SPOILER
I think Ratbastid has a point. While I may be missing some plot detail, I do remember Agent Smith leaving the Matrix in Neo's dream. Neo could simply be seeing the future again just as he saw Trinity being shot, which could still allow Bane's actions to follow the plot correctly. Suppose Bane was never infected. Suppose he is simply a normal human who just so happens to be particularly evil. Neo's dream might show that subconciously Neo knows this, but for this to be true, Neo must have had spent some time with Bane. This might be cleared up in other Animtrix shorts or even the game. Neo's dream might just show that Bane isn't infected until Revolutions. He is still dangerous though, since for Neo to dream about such a terrible thing happening, he must be all kinds of crazy. This could even be the reason Smith chooses to infect him. I'm probably way off...
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