Continuity mistake: When Seth has been sliced by the blade, he spits blood that goes all over his face. It then cuts to Hoffman looking at him, then back to Seth, and now the blood on his face has gone. This happens three or four times. (00:05:10)
Continuity mistake: As Ben and Jane drive down the road, it is raining. After they hit the ghost, the scene fades to black. When the scene fades back in, it's heavily snowing, and a previously nonexistent thick sheet of snow is covering the ground. As they get out of the car, they start talking. During their conversation, there is a quick cut, and with this, it instantly stops snowing.
Continuity mistake: When Dacyshyn drags Mulder by his legs and brings him to the shed, he goes past the tree stump with an axe embedded in it, but in the close-up of Mulder's torso there is some debris on the tree stump and the axe has disappeared, then the axe reappears still embedded in the wood. (01:31:10)
Continuity mistake: When the Jeep stops in Priceton, we can see its on a single land road. However once it starts to accelerate in the next shot to ram the tree at the intersection, it is now a forked road.
Suggested correction: The road is a standard two way road that is unpainted with road markings. Almost all non major roadways are unpainted and many of them fork into two separate roads.
Continuity mistake: In the scene where Benjamin drinks tea with a woman every night and they have a conversation, the woman's tea glass has varying levels of tea in it between every cut during this scene.
Continuity mistake: In the scene where Hud, Jason, and Rob are hiding in the grocery store, you can see several items toppled over on the shelves above Jason's head. When the lights start to flicker, you notice almost all the objects are now standing upright, only to be toppled over again. (00:21:45)
Continuity mistake: At one point, when Leon is fighting with Mahogany on the train, there is a shot of blood dripping off a knife onto Leon's face. This blood later vanishes. (01:20:02 - 01:21:19)
Continuity mistake: When the Porsche Cayenne is racing through the junk yard, in one shot the right headlamp is broken. In the next, it is fine again and then it's broken once more.
Continuity mistake: When the "substitute" boy gets off the train he is with an older women. The reporters ask the mom and boy to take a picture together. You can see from the camera angle that the older woman is in the background when the flashes go off taking the picture. Later in the movie, the psychiatrist holds up a newspaper article with the picture in it. In the newspaper picture, the older woman is not in the background.
Continuity mistake: After speaking to Donald's mom, Sister Aloysius is standing in the wind with leaves floating in the air. The quantity of leaves situated on the ground changes between shots. (01:17:55)
Continuity mistake: When Wyatt is shot, the amount of blood on his shirt next to the collar increases, decreases and even disappears between shots.
Continuity mistake: When we first see Agent Holloway viewing the crime scene photos taped to the wall, he is facing camera looking at transparent pictures on a transparent wall (as if we are behind that wall, seeing through it). When the angle changes to see the Agent from behind, the photos are now paper photos on a normal, opaque wall and the pictures are arranged somewhat differently - most notably to Holloway's right near the top where two wider photos are vertically aligned atop and below each other in the second shot when they were misaligned in the first shot by nearly half their width. The transparency versus opaque materials issue is a stylistic choice of the director and not a mistake, but the mismatched alignments is a mistake. (00:11:25)
Continuity mistake: 50 Cent goes through the window onto the floor below. There is glass and debris everywhere. Our heroes run past him later and there is no sign of the window debris.