Continuity mistake: In the beginning of the film John and Detective O'Hara are driving. She suddenly gets really sick, so John stops the car so she can get out. She runs and then throws up. When she comes back to the car she trips on a log that was never there before. (00:19:45)
Continuity mistake: On Kimble's first day as the kindergarten teacher, he's wearing a white shirt with jeans and a jacket. When he shows up the next day and is talking with the mother of one kid, he's wearing a maroon shirt with khakis. They then cut to the kids doing the pledge of allegiance, then to the kid eating everybody's lunches. In that shot Arnold is wearing the white shirt, jeans, and jacket. But then, they cut to "Who is your daddy, and what does he do?" sequence, and Arnold is back in the maroon shirt and khakis. It seems the "Lunch-box kid" part was in the wrong spot.
Continuity mistake: Toward the end of the film while the school is on fire, Kimble's partner runs to the side door gun drawn. She is spotted by Crisp's mom and is hit by her car, knocking her down. When she arrives shortly with a bat to save Kimble she is much more banged up than when she was first struck, most noticeably a rip on her right shoulder that wasn't there before.
Plot hole: Cindy manages to pick Crisp out of a line-up even though she was hidden in a box and didn't see him, she only heard his voice. But even with that, he isn't asked to speak during the line-up.
Continuity mistake: In the scene where Phoebe is interrogating Cindy, Cindy refuses to testify or identify Crisp in the line up. She then tries to leave the interrogation room, but it's locked. When the interrogation is over, we see that Phoebe opens the same door without any problems, or anyone opening it from the outside. (00:08:38)