Continuity mistake: When Harrison Ford confronts (and beats up) the tourists, there are a number of close-up shots of the people in the first wagon, including one where Viggo Mortensen leans forward and tells the driver to do nothing, even though he is being provoked. In all these close ups, Mortensen is bare-headed. When the shot changes to Ford's perspective, from the cart behind, we see one of the tourists grab a straw hat from Mortensen's head. The hat has appeared out of nowhere in a split second. There is a child with a straw hat behind Mortensen, but the hat stays on his head in both shots. (01:22:50)
Continuity mistake: When Samuel shows his new toy to Rachel she looks out of the kitchen window into the fields. Two shots later she looks out of the same window and, surprise, there are Eli and John putting up the bird house. When she talks to Eli later there is same window in the background, with no bird house to be seen. (01:23:50)
Continuity mistake: On the way from Lancaster to Philadelphia the length of the train changes. It's fairly long when it enters the Lancaster station; after leaving the station, in one shot it's just a locomotive and one car, while in a later shot it's a locomotive and three cars. (00:09:00)
Continuity mistake: When Schaeffer and the bad cops approach the Amish Farm, it's late afternoon/early evening. But when Samuel runs to the Hochleitner farm, and when the other Amish come running, it is mid-day or early afternoon.
Continuity mistake: When Rachel dances with John Book, she is chastised by her Father-in-law outside the house. As the camera angle switches back and forth from over his shoulder, then hers, the distance between them is radically different. Over her shoulder the brim of his straw hat is nearly touching her. From his perspective there appears to be a good three feet of distance. (01:05:00)
Continuity mistake: When John puts up Rachel and Samuel with his sisters they are shown to their bedroom. The sister goes down the stairs and says a few words to John before he leaves. When she comes back Rachel and Samuel have already changed into their nightgowns - not at all enough time for that. (00:21:15)
Continuity mistake: When the local bums provoke the Amish, Viggo Mortensen's hat is grabbed twice - for the first time when the leader of the gang smears Alexander Godunov's face with ice cream, the curly-haired guy can be seen swiftly grabbing Mortensen's hat in the background. Thereafter Mortensen is hatless - until the same curly-headed bum grabs his hat again, now in the wide shot. (01:25:05)