When Donald Kaufman goes through the windshield, you hear the sound of regular glass breaking. You can also see a pane of glass break off the car. Real windshields don't break like normal glass does. It doesn't make a shattering noise and doesn't shatter like window glass.
When Charlie Kaufman opens the passenger (right) door of the rental car, we hear a buzzer, warning that the key was left in the ignition. The buzzer should only sound when the driver (left) door is open.
Immediately before Charlie Kaufman has a tantrum in the New York hotel room, the lamp to the right of the bed can be seen leaning against the wall in the corner, but it is standing upright before he knocks it over in the next shot.
At breakfast, when Donald Kaufman, Charlie Kaufman, and Donald's girlfriend are in the kitchen, the coffee pot keeps switching sides of the table. Also, none of the characters ever fill up their cups with coffee, but suddenly Donald and his girlfriend have full cups of coffee.
When Susan Orlean and her husband are having the dinner party at her home, she excuses herself from the table to go to the bathroom. When she closes the door and slides to the floor to sit, she puts her left hand to her face and her wedding band is on, then it's not on as she slides to the floor to sit, and then in the next scene when she is sleeping in bed, it's on again.
When Charlie Kaufman and Donald Kaufman talk about the serial killer in the script of "The 3" being a literature professor, Charles' hands are clasped. In the close shot of Donald with Charles in the foreground out of focus, his arms are folded.
When Charlie Kaufman is getting take out from the restaurant and bumps into Valerie, he leaves the restaurant in a hurry and does not take his bag of food with him. In the next scene, we see him eating the food.
In the swamp scene when Susan Orleans is cradling John LaRoche's head, the hair on his forehead is totally disheveled. Then in a closeup, his hair sweeps neatly across his forehead. Back to the wider shot, his hair is disheveled again.
In the beginning of the film, when John La Roche is trudging through the swamp searching for orchids, he is seen up to his armpits in water. Once out of the water, when the park enforcement officer approaches them, the water line on LaRoche's shirt is clearly seen as just above the waist - about a foot lower than the point to which he was submerged.