Revealing mistakes: During the deserted island hotel scene, a red vehicle can be seen traveling in the background behind the hotel.
Continuity: After Hennessey and the Stooge are rescued from the pirates, and Team Zissou are in the midst of a shoot-out behind an old jeep, Hennessey is clearly wearing flip-flops. However, when the team reach the boat, he has gained a pair of brown boots.
Continuity: After Hennessey and the Stooge are rescued from the pirates, and Team Zissou are in the midst of a shoot-out behind an old jeep, the position of the snake changes between shots.
Continuity: When Hennessy is speaking to Steve on his boat, there is a stain on his yellow couch that disappears and reappears in between shots.
Continuity: Steve peels the tape off Bill Ubell's mouth when he rescues him from the pirates, and several days' growth of beard is plainly visible. Moments later, when they are running toward the beach and they reach the boy cooking lobster over a small fire, Bills beard is noticeably thinner.
Factual errors: The word "terrified" is misspelled as "terrifed" in the subtitles early in the movie.
Continuity: When Ned is shining his shoes in his cabin and Steve comes to speak with him, the clock goes backwards between shots from 9:50 to 9:40.
Revealing mistakes: The "Belafonte" model is shown with an observation dome built onto the bow of the ship. It is also mentioned by Zissou. When the ships bow is exposed cresting a wave, there is no evidence of any structure below the waterline at the bow.
Continuity: When the team is in the submarine towards the end of the movie Steve's hands are on the steering wheel. As the neon fish swim towards the sub (from the crew perspective) you can see the steering wheel without any hands on it, but when the jump to Steve, he hands remain on the wheel.
Revealing mistakes: When Steve and Ned are in the helicopter, they're supposedly far out in remote "unprotected waters". There's a two-masted sailboat visible over Steve's right shoulder in several shots. In the same sequence, the water beneath the helicopter is shallow and churning with brown sand, indicating this was shot very near a beach.
Continuity: While on the submarine, Zissou inserts a tape into the player. The clock reads 2:18. The camera immediately cuts to Zissou turning the volume up, but the time now reads 1:45.
Crew or equipment visible: As Steve and Ned walk through the ship, after Steve surprises them in Jane's cabin, they walk past a white picture in which the camera is reflected.
Crew or equipment visible: During long dolly shot in the end credits, when Steve is walking left to right with the young boy on his shoulders, you can see the camera crew shadows pass in front of them several times.
Audio/visual unsynchronized: After the pirates leave and Steve finds the dog still on the ship, we hear Cody bark, but his mouth doesn't move.
Errors made by characters (possibly deliberate errors by the filmmakers): When reading the six volume novel to her unborn child, Jane is holding one volume in her hands while six others are lying on the chair, which makes it a seven volume novel.
Continuity: After Hennessy is rescued from the hotel, a long blood stain is seen on the back of his white t-shirt. By the time he reaches the boat, the stain is gone.
Continuity: When Hennessey is negotiating with Steve on his boat, the angle of his Powerbook's screen - well out of reach - changes between shots.
Continuity: The team's Glock automatics frequently turn into Berettas when being fired. This is very noticeable during the rescue of Hennessy during the card game, when Zissou draws a Glock, but in the next shot he is clearly firing a Beretta Model 92.
Continuity: As Steve is leaving Hennessey's ship, you see the shot from inside, the door is open and though you can't see out, light coming in, indicating that it is nice and sunny out. As Steve leaves, you see outside, it is raining and there is no light to shine inside the vessel.
Continuity: During the film festival Q&A at the beginning of the movie, Steve Zissou needs a translator to understand questions asked of him in Italian. Shortly afterward, while in the adventure club with Ned, Steve can perfectly understand men gossiping about him in Italian from the next room.
Continuity: When Steve pulls his gun on Jane during the interview, there is an audible thud as if he'd pulled the gun and then lowered it to touch the table, however when the shot changes to face him, he is holding the gun well above the table's surface.
Revealing mistakes: In the fax to Operation Hennessey alerting him of the alarm going off at the sea lab, Headquarters is spelled "Headquaters".
Errors made by characters (possibly deliberate errors by the filmmakers): Owen Wilson's character supposedly grew up in Kentucky, however he pronounces Louisville as "lou-ee-ville". The locals always pronounces it "lou-uh-ville".
Revealing mistakes: When the crew is examining the sunken aircraft, we see the black box which is labeled "Black Box". In reality, airline "black box" flight recorders are colored bright orange.