When the train is stopped by the police - during the whole time the policeman checks the passenger list - the filming inside the train is accompanied by train wheel sounds, suggesting it is moving (actually quite fast).
Mrs. Froy (Richard O'Brien) is shot several times by Yamashita (Togo Igawa) including one gunshot to the head, but in a later scene when Mrs. Froy is laying dead, the gunshot wound on the head has disappeared.
The Christmas package holding the box moves between scenes. When Steve Zahn first removes the box the package is on the floor, the camera switches to a long shot, we see the package back on the man's lap and so forth throughout the scene of everyone picking up and looking into the box.
In a scene the old lady gets shot a few times, once in the head in the middle of her forehead. Then other characters are shown and then when the dead body of the old lady is shown again the she has no damage to her face whatsoever.
After Miles leaves to notify next station about the dead man, Peter approaches the corpse. On the close up you can see the chest moving because of breathing and not because of the movement of the train.