Check out the part when the train bashes Agent Smith. When Neo begins to head for the exit you hear the same train jamming its breaks. First of all its takes about 10 seconds for a passenger train to halt, not 3. But whats really confusing is that Agent Smith walks out of the train about 6-7 carts away from the first one. How did he stop the train if the only way to stop it is in the first cart? That'll give you something to think about.