Plot hole: If Jack can speed the train up at the end, why does he not try to slow it down? Even if it can't be stopped completely, using the speed lever to reduce it to the minimum possible would be a sensible course of action. There is nothing to suggest he wouldn't be able to do this as he is able to increase the speed without any trouble. If there was something to show that slowing down the train would be unworkable it would make sense, but seems to more serve as a plot device.
Plot hole: When they get Sam the driver off the bus and onto the trailer, it's stressed how important it is to get him to hospital, but in all subsequent scenes, the trailer never leaves the side of the bus and no-one takes Sam off.
Plot hole: Payne's finger prints would've been all over the elevator, on his shotgun, and near the area where he killed the security guard as he was never shown wearing gloves. Since he was a former police officer, I would assume his prints would've been on file with the FBI and in a multitude of databases. You would think they would've been able to identify him much earlier in the movie than they did by running the prints through all databases of finger prints.
Plot hole: The police thought they could catch the bomber at the ransom drop because he did not know that the bus had exploded. However, the exploding bus would have created a huge plume of smoke that would have been reported by the media. (01:30:00)
Plot hole: It is never definitively stated if the bomb is tied directly to the axle, triggered by the speedometer instrumentation or throttle. Regardless, as long as the wheels keep spinning above 50mph the bomb will not explode by design. This means that if you lifted the wheels of the bus off the ground or you bottom out, you could keep accelerating without any speed at all. This could be accomplished in any number of ways. One example would be driving on grass and keeping the tires spinning.