When Lisa comes home after the accident, throws up and hugs her mother, there's no blood on her arms and hands. In the next shots under the shower, there is plenty.
When Paul is at her home, his sleeves are rolled up, and when the camera is in front of him the sleeves are down.
Between frames, Damon holds Paquin's hand, then not.
When Lisa visits her math teacher at home, her hands move between shots: when she is seen from behind the teacher her her arms are crossed, in the next shot they are beside her body, then they are crossed again.
The front and back of the door to the driver's house do not match.
On Lisa's geometry test, question 2 doesn't make sense. It should read "find WA" or "find WY".
In debate class, Lisa mentions that 3,000 people died during the 9/11 attacks on the World Trade Center. The actual body count on that day (including the hijackers and excluding people who died of related conditions after the attacks) was 2,996, but Lisa's statistic is clearly intended as a close estimate.
There's a close-up shot of a New York Times article about the bus driver. The article says he works for the Metropolitan Transit Authority. The correct name is the Metropolitan Transportation Authority.