At almost the very end, when the two survivors enter the last tunnel, there is a shot from behind them. The other end of the tunnel isn't visible, which would make sense if it was extremely long (the opening would become a pinpoint, or smaller) or there was a turn in it. But when the soldiers see the survivors, they also can clearly see the light at the end of the tunnel, where they entered, and it is shown as a straight tunnel. If the soldiers could see the survivors and the tunnel opening they entered from their end, the survivors would have been able to see the light and exit from the opposite end as well.
When the final victim falls to their death from the back of the train, they are within the safety rail. They only move outside the rail at the instant they fall. They would have had to climb over the rail. They couldn't simply fall forward as shown.
Seok-woo (the father) has consistently differing bloodstains on his shirt in different scenes (most notable after the multi-car trip to get back to the front). Also, the bloodstains appear very light on his shirt, like watercolors, rather than thick, dark, clotted blood.
In one scene, a window is clearly seen without any blood on it, yet in the next shot, from the inside, there are many blood stains on it.
At the 74-minute mark, when the passengers are trying to close the door and block the zombies from gaining access to their wagon, the door is almost closed, then half open, and then almost closed again.
When the train operator starts another engine at the station and he gets off to save a passenger from zombies, the engine keeps moving at the set speed. All train engines have fail safe systems that prevent them from moving if there is no personnel on board.
For a train to travel to its destination over vast distances someone, usually an operator from a remote location, needs to keep the track switches on path. From what this movie depicts it is unlikely that the switch operator will stay intact long enough to make the train travel this far and still make it to its destination.
Everyone seems to be able to make and receive calls with ease. In reality, a national emergency with chaos on that level would surely cause the national cellphone network to overload, and that's ignoring the many cellphone masts that would be abandoned by technicians or overrun by zombie attacks.
The abilities of the infected seem to change for the convenience of the plot. For example, before they claim the infected will only attack if they see you, Sang-hwa traps an infected man in the toilet and it still tries to attack him, despite not being able to see him. Also, it is clearly shown that the doors aren't automatic as the handle needs to be pulled down, but eventually they realise that the infected can't open doors, but during the initial outbreak several do so with ease.
It's shown late in the movie that the toilet opposite the pregnant women wasn't locked. Soo-an never needed to walk to the end of train.
Her entire plot was pointless.