When Kirk is pitching his movie to Lorelai, he says he can edit out 2 of the hells, but he needs to keep the damns. Later, when the movie is shown, neither of these words are in it.
Obvious audio edit when Rory says "wherever" when she and Jess are riding in the car after getting ice cream.
After Luke arrives with the brownies and he and Lorelai start walking toward the kitchen, a sound engineer and mic can be seen through the front door.
When Jess enters the principal's office, he closes the door and you can see a hand reach out and grab the door just before it closes.
When Christopher calls Rory, he says he has to cut their call short and to add 40 minutes to his call the next week. When they hang up, Rory says she is late for school. If Rory was late for school, it wouldn't be possible for her to talk to her dad for another 40 minutes, and it makes no sense for them to have a call scheduled at that time.