Crew or equipment visible: When Clementine and Joel see each other again at the diner near the beginning of the movie, the shadow of the camera is visible off to the left.
Revealing mistakes: Members of the public can be seen waving to the camera while Joel is driving in his car.
Continuity: During the "operation", Mary passes a joint to Stan. In the next shot, Mary has the joint again.
Continuity: Mary's hair changes from "windswept" (long shots) to neat (close-up) and back again when talking to Howard outside Joel's apartment, after Howard's wife catches them together and drives off.
Revealing mistakes: When Clementine goes to Joel's building foyer, and meets Joel's neighbor (the "McRomance" guy), the actor waiting to walk into the scene is reflected in the door.
Crew or equipment visible: When Clem gets out of the car to get her toothbrush, a mic pack is clearly visible under her shirt.
Continuity: Near the end of the film when Mary is walking around the corner with her box of belongings and cassettes, the man walking directly behind her disappears for one shot.
Continuity: When Clemetine and Joel are meeting on the train in the beginning, the hair around Clemetine's face alternates from being neatly curled to being more frizzy and separated.
Continuity: When Joel and Clementine first talk to each other in the train, Joel says, "I was trying to be nice." At that moment the train is passing an urban area. In the next shot, the train is in a heavily forested area.
Continuity: When Mary first comes to Joel's apartment to visit Stan and Patrick, she goes into the kitchen to pour drinks. Just after she says "Let me do the honors," the pendulum of the clock on the wall is not moving. About 2 seconds later, as she is pouring the drinks, the pendulum on the clock is swinging.
Continuity: When Joel and Clementine are eating at the Chinese restaurant, Kang's, the beer level in Clementine's bottle change between shots. Clementine pours some beer into a glass and the bottle is obviously about 3/4 empty. When you see her set the bottle down in a shot from behind, it is almost full. Immediately in the next shot from the front, the bottle is almost empty again.
Errors in geography: Long Island Railroad trains are shown with a red stripe on the cars. This is the livery color for Metro North trains. LIRR trains are blue.
Continuity: In the beginning of the movie, as Clementine is walking on the beach, you can see her take a couple of steps on the wet sand near the water, but in the next shot, as Joel is looking at her, she is standing on dry sand.
Factual errors: During the credits, the car radio shown is from a General Motors vehicle rather than Joel's Toyota.
Continuity: In the scene where Mary first comes into Joel's apartment, Patrick and Stan had been drinking beer. At first, just before the door is opened, they are both Rolling Rock (green bottles). After she has entered, Stan's beer turns into a Labatt Blue (brown bottle).
Errors in geography: While on the train on the way from Montauk point, Joel and Clementine are shown to ride the train to their destination of Rockville Centre, NY but the Montauk branch of the Long Island Railroad only spans as far as Babylon, NY (a full 12 stops away from Rockville Centre, NY).
Incorrectly regarded as goofs: When Clementine asks if she is ugly, Joel calls her "Tangerine" after the scene where she died her hair orange and he gave her this nickname. The film shows Joel's memories of Clementine working backwards from when she left to when they met, so Clementine would not have this nickname yet. However, because Joel is conscious of his memories (as well as manipulating them consciously at the time) and had heard Patrick in the previous scene calling Clementine by this nickname, it's possible that he calls her "Tangerine" for this reason.
Factual errors: Valentine's Day 2004 was a Saturday, but the platform where Joel is waiting for the train is full of commuters.