When the train approaches, Walt, Jesse, and Todd are under the bridge as it passes over; it has not started to brake yet. Shortly after that shot, the train comes around a slight bend and the engineers see the truck and apply the brakes (in reality when shot, the train is actually approaching the bridge again). At this point there wouldn't be enough time/distance for the train to stop before hitting the truck. When measuring the distance earlier, Jesse states "814" as the distance from the road to the bridge. It's likely 814 feet (in reality, it is). Regardless if that's 814 feet or meters, the train couldn't cross the bridge at speed and stop in time.
The shot of the excavator lowering the tanks in the ground is at a different location. In that shot, there's a good amount of grass behind the pile of dirt. In the next shot when the water truck is backing up to the buried tanks (and in other wide shots of the buried tanks) no grass is nearby.
As the team waits for the train, there's a high shot of the trestle with the shadows going to the left (when looking in the direction of the oncoming train). A few minutes later, when the train passes over the trestle, the shadows go to the right,
The locomotive's horn sound constantly changes before, during, and after the heist.
The train traveling from California to Texas is a shortline freight train. In reality, it would be a BNSF Railway mixed freight train that would be much longer than the one shown. It would also be running (from descriptions by Lydia) on a modern double-track mainline, not a single-track shortline.
The train is going from California to Texas, heading East. The shadows in the northern hemisphere will be pointing generally North, yet Walter points to the East and says 'the train will be coming from that direction'.
When Jesse is measuring the tracks, they don't know yet which car the methylamine will be in. Therefore, they can't really know that this particular car will be on/near the bridge when the train stops. However, they would have a general idea based on past data.
When the guys start robbing the train and Walter gets the lids off the containers he gets dirt into it, making the methylamine unclean.
Hank tells Walt Jr. that he just got the Blu-ray for Heat (1995). However, "Dead Freight" is set in September 2009, while the Blu-ray for Heat wasn't released until later that year in November.
When the train conductor is getting ready to start the train back up, he pulls the whistle lever twice, but we hear it sound only once.
During the heist, water is pumped into the tank car at the same time methylamine is pumped out of it. Since the water is heavier, it would fall to the bottom and be pumped out again, diluting the methylamine.
At 22:41 -Holly clearly says "Mama" but both adults totally ignore her.
The truck on the tracks has a "healthy" battery when the driver cranks it. The 2 train engineers should think to crank it with 1st gear in the gearbox, so the truck could move forward slowly, out of the train tracks.