When Mr. Fogarty and Charlie are talking to Tom in the diner, you hear audio of Charlie saying "You know what he does to people he doesn't like." Onscreen his mouth doesn't move. Obviously dubbed in later.
(at around 13 mins) When Carl Fogarty first shows up at Stall's Diner, he tells Tom/Joey that his name is 'Joey Dewsack' (mispronouncing 'Cusack' twice). It is most pronounced the second time he says it.
When Sam the Sheriff comes to the house for the second time (after the second batch of killings), he parks diagonally at the beginning of the driveway, essentially blocking the entrance to the driveway. He and Tom/Joey go into the house to talk, and while they are talking, Edie pulls into the garage, parks and comes into the house. She could not have pulled into the garage with the Sheriff's car blocking the driveway.
When Sam (the Sheriff) stops Fogarty's car and talks to him, he looks at the driver's license in his hand. Immediately afterward, Fogarty closes the window, and the car drives away, without Sam returning the license. Yet his hands are empty.
While Tom is in the hospital after the shootout at the diner, his wife shows him the front page of the news paper with him on it. Not possible for the newspaper to write/print and deliver the paper that night before his wife makes it to the hospital.
In the beginning of the movie when Tom (Viggo Mortensen) is going to the diner, he crosses in front of what looks to be the Middlebrook courthouse. It is supposed to be early in the morning, but the clock on the courthouse is showing 1:15.
Early in the movie, Tom and his family are sitting to breakfast. Tom pours some orange juice into his glass and sets the pitcher down. The view cuts away, but when it comes back the glass is much fuller than it was before.
While Jack is being bullied by Bobby Jordan after the softball
game, he puts on his shirt. In the next over-shoulder shot we can see his bare neck and shoulder, clearly implying that he doesn't have a shirt on. When the shot cuts back to the other shot Jack has his shirt on again.
In the locker room confrontation scene between Jack and Bobby, a front shot shows Jack crossing his arms in front of his chest as he leans against his locker. The scene immediately cuts to a rear right view and we see that both arms are hanging by his side.
When Tom is driving from Indiana to Philadelphia, a sign in the highway lists the travel distances as "Indianapolis 36", "Columbus 247" and "Philadelphia 680". But Indianapolis in 170 miles west of Columbus and 585 miles from Philadelphia, so if he is 36 miles from Indianapolis, he's only 206 miles from Columbus and 611 miles from Philadelphia.
As Tom lies in the hospital and talks about being Joey, Edie goes into the bathroom to throw up. When she comes out, she has a tissue in her hands. The tissue disappears and reappears over the next several shots until she finally throws it down on the floor and leaves.
When Tom throws the pistol into the pond, we are looking at him from the front. He tosses the pistol into the water out and to his left. In the subsequent shot, we see him from behind. The ripples in the water from the gun are out and to his right.
After Tom kills Richie there is a shot of Richie lying dead. Richie's mouth is partly open. When we cut back to Richie a moment later, his mouth is closed. In addition, the shot of Richie with his mouth closed establishes his arms in a downward position, whereas the next long shot shows them raised over his head.
When the sheriff visits Tom at his house to discuss his doubts about Tom's story, Tom is working on his truck, which is not in running condition. Tom stops his work at that point and does not return to it, but that same night he gets in the truck and drives hundreds of miles to Philadelphia with no problems.
In a close-up shot during the final scene in the dining room, Edie is shown serving a spoonful of corn onto her daughter's plate. In the next wide shot, the corn is gone from the daughter's plate and Edie once again puts corn on it.
Towards the end of the film, Richie kills Ruben who is lying on the floor ("How do you fuck that up"). His pistol's slide doesn't move when he fires the shot. (On real pistols the slide moves back to clear the used cartridge)