The Guard said:
How can he not see it? The two are right on top of each other. It looks for all the world to me like Ra's bashes him in the head, and while Batman is momentarily stunned, uses the cane himself.
Trust me on this.
When Ra's says "you can't stop this train", it's in part because he's choking him and has the upper hand, and in part because he himself prevented it from being stopped by screwing up the controls. After Batman breaks Ra's sword in two and kicks him backward, he goes to the front of the car to stop the train. Ra's, seeing him do this, uses the piece of the jagged cane he's still holding to either hit or stab Batman in the back, and sends Batman off balance for a second. Ra's then uses the cane to jab at the controls, lodging it there, and resumes his attack on Batman. When Batman says "Who said anything about stopping it", he's referring to the fact that he doesn't have to because of his backup plan with Gordon. Yes, Ra's looks up and you see the controls that he shot out (this is a plot device to remind the audience that the cane in the controls thing happened, so that the audience knows the train is going to keep going). Then Ra's notices that the track itself is falling to pieces. And realizes what Batman is talking about. This momentary shock gives Batman the edge to gain the advantage.
After thinking about this over and over, and watching it over and over in my head, I really think Guard has hit the nail on the head. The flow of events could have been more clearly shot, but the confusion is what Nolan was going for, and in part I think it was to make this ambiguous.
Batman breaks Ra's's sword.
Batman tries for the controls to stop the train.
Ra's goes after him, fighting ensues, and Ra's jams his broken sword into the controls.
Cut to Gordon blowing out the track support.
Ra's starts choking Batman, and says "Nothing can stop this train now." Direct reference to him fouling the controls.
Batman says "who said anything about stopping it?" In order to redirect Ra's' attention to the crumbling track out the window.
Batman gets upper hand due to this distraction, and gets on top. "I won't kill you, but I don't have to save you."
Throws batarangs, and escapes. In other words, Batman's backup plan worked, and it was an unfortunately high-damage plan.
Emergency brakes are a plot hole, unless you assume those were the controls Ra's broke - which seems obvious since Ra's talks about stopping the train, and there was no throttle in the controls Ra's broke. Besides, emergency brakes probably would stop the train right inside the tower, as fast as it was going.
The only real plot hole is why Batman didn't just go for the emitter and blow it up with his mini mines at first - countered by his desire not to blow Ra's up along with it.