Continuity mistake: When the crew is in the submarine and they're just about to see the shark, Steve is holding on to the steering wheel. But when the view is of the steering wheel and little windows, no hands are on the wheel. Cut back to the crew, Steve is once again holding on to the wheel.
Continuity mistake: During the shoot out with the pirates on their secret island, Team Zissous' firearms change from Glocks 21's to Beretta 92FSs'. When the members are holding the guns without firing, they are in fact Glocks. Any scene where they are actually shooting, they are holding Berettas.
Continuity mistake: Warning: Spoiler. Following the shootout with pirates at the abandoned hotel, it is raining hard as Team Zissou makes their escape. When they arrive at the beach, it has suddenly stopped raining. There has not been a lapse of time, as the action on the beach is a continuation of the running sequence. Secondly, we see a young boy cooking something over a campfire. There is no way he could have built a fire in the heavy rain that was falling just a moment earlier.
Continuity mistake: In the party after the film, we see "Jaqueline" crossed by a simple line. When Zissou is asked about who she was, the crossing is an X.
Continuity mistake: When Steve talks with Ned in his room, the clock behind Ned jumps from 9:40 to 9:50.
Factual error: In the submarine scene, the crew is sitting in a well illuminated cabin and the surrounding ocean is pitch black. They couldn't possibly have seen the shark outside because of the window's mirror effect.
Continuity mistake: When Alistair Hennessey is lamenting with Steve Zissou about pirates aboard the Operation Hennessy vessel, there is a shot of Alistair lounging on a yellow sofa. To the left of the shot there is an opened silver laptop, but when the camera quickly cuts back to this shot, the laptop is in a semi-closed position. (01:04:45)
Visible crew/equipment: When Ned and Zissou are arguing and walking through the boat, they pass in front of a picture where the reflection shows a completely different camera set up from the documentary crew, with two grips wheeling a dolly.
Revealing mistake: The camera occasionally pans sideways through walls as characters travel from room to room. In two instances, a visible edit can be seen between the rooms, revealing that they are not in fact adjacent parts of the set, but rather were spliced together. In the latter of these two, an electrical outlet disappears mid-transition.
