When the Philadelphia cops are talking on the phone to the cops in Lancaster, first the Lancaster cop pronounces Lancaster (lank aster) like the county inhabitants do, but in the next breath, he pronounces it LANcaster like everyone outside a 25 mile radius does. Is he local or isn't he?
After Book drives into the birdhouse, and Rachel opens the car door, Book's wound has bled down his right pant leg nearly to his knee. When Book is placed on the wagon, however, the wound has not bled down his pant leg.
The first time Book goes to Strasburg with Eli to use the phone, the initial shot shows the horse and buggy pulling into a "parking space." On the next shot, we watch John exit the buggy and walk toward the phone. As John passes the horse, we see that the horse has been been chained to hold it in place. As John passes the horse and group of people, we see Eli exit the buggy, then walk up to join the group. How the horse got chained, or who did it, is unexplained.
When Rachel fetches the gun from the cupboard to hand it to Book, a number of pantry items are visible that no self-respecting Amish would have in their cupboard (Campbell's soup cans, packages of Jell-O and other boxed products).
When Rachel brings John lemonade in the wood shop, John says he is trying to fix the birdhouse that was broken. However, he is planing a large board that resembles a door. Unless he was doing other work for Eli besides the birdhouse, it seems odd he would be doing this.
During the breakfast scene after John milks cows, Eli uses an office chair with wheels to go from the stove to the table. It is unlikely that Eli would have been able to obtain such a chair (whether from an office supply store, thrift shop, salvage yard, etc.) given the Amish have little contact outside their community.
At the time this movie was made, Amish carriages were not required to have reflectors. Since then, an agreement between the Pennsylvania Department of Transportation and the Amish community has required the reflectors to be present.
When Samuel is hiding from McPhee in the bathroom cubicle, he stands on the toilet seat, holding the two toilet walls. At first glance, it would seem that his fingers are on the top of the walls (and would therefore be easily seen by McPhee in the next cubicle), but closer examination shows that his fingers are actually beneath the top of the toilet wall as is the hat in his right hand.
When Samuel is in the toilet cubicle and makes a noise after the murder, McFee hears the noise and starts to check the cubicles. Fergie says "I already did that." But if he did he would have seen the boy who was there before they came in.
When Carter pulls the police files on Samuel and his mother, he finds a folder marked "Rachel Lapp" and removes it. He then flicks past a few more files and finds the one marked "Samuel Lapp". Although this might be correct if they were in alphabetical order by the entire name, the files would be more likely to have been held in order of surname, then first name, so the files would probably have been held consecutively.
Near the end of the film, when John Book is saying good-bye to Samuel, they are both shown full-front, sitting in the grass, with a farm pond right in front of them. Yet, when Book gets up to leave, the two are being filmed from behind. Book stands, then walks directly away from Samuel. The pond has disappeared.