Errors in geography: Nigel, the Pelican, is a Brown Pelican, scientifically known as Pelecanus occidentalis. The movie is set in Australia, where there are no Brown Pelicans, instead there is the Australian Pelican, scientifically known as Pelecanus conspicillatus. Both birds look quite different.
Errors in geography: The diving flag seen on the dentist's boat is the United States' "Diver Down" flag (red with white stripe). This flag is not used in Australia, and would not be seen on the Great Barrier Reef. The Australian version is blue and white.
Factual errors: When the fish are in bags and the bags are in the ocean, the bags should float with their inner water level at just about the same level as the surface of the ocean.
Factual errors: Marlin and Dory are advised to swim to the back of the whale's throat and then are blown out of the whale's blowhole. This is not physically possible as whales mouths and digestive systems are not connected to their respiratory system and blowhole.
Factual errors: Coral should be bigger than Marlin. Female clownfish are always bigger than their mates (often twice as big).
Continuity: When the dentist is scooping Nemo out of the aquarium with the bag, the first time we see the bag it has a zipper top. The next time we see the bag outside the aquarium it is a plain bag with no zipper top.
Factual errors: The divers' boat has a stern-drive unit with two propellers. When it starts, both propellers turn in the same direction, but they should rotate in opposite directions.
Continuity: When Bruce is chasing Marlin and Dory, the mask in his mouth switches from the right side to the left side and then back again.
Continuity: When Nemo swims on top of Mr. Ray in the school scene, he disappears behind the right eye to reappear at the back at the end of the scene.
Errors made by characters (possibly deliberate errors by the filmmakers): When the fish in the tank are watching the dentist work, Bloat asks if the rubber dam and clamp have been installed. Another fish replies it has, but when the patient is shown, it is not present.
Factual errors: Bloat (Long Spined Porcupinefish/Diodon holacanthus) and Jacques (Cleaner Shrimp/Lysmata amboinensis) shouldn't be in the same tank because invertebrates are the Diodon holacanthus' main food.
Continuity: When the Goggles fall off the divers boat at the start of the movie, they fall down vertically, yet the submarine wasn't near the reef.
Errors made by characters (possibly deliberate errors by the filmmakers): When Mr. Ray sings his "Let's Name the Species" song, he isn't actually naming species. Porifera, Coelenterata, Ctenophora, Bryozoa, Arthropoda, Echinodermata, and Chordata are all phyla. Hydrozoa, Scyphozoa, and Anthozoa are classes in the phylum Cnidaria (Coelenterata), and Gastropoda is a class in the phylum Mollusca. The order of classification is: kingdom, phylum, class, order, family, genus, species. Phyla and classes are definitely not the same as species, although it is revealed, in the DVD, that Mr. Ray isn't an actual scientist, more that he just picks things up. In that case, it could very well be that he mistook the one for the other, not knowing that he was passing on incorrect information.
Factual errors: The instrument that is used by the dentist that is mentioned in the movie is called a "gates glidden" instrument not a "gator glidden drill". It is also mentioned that the dentist uses it to access the root canal. It is not used to access the root canal but rather to clean and shape it. The proper instrument that is used for endodontic access is a carbide bur.
Continuity: When Nemo first enters the tank and he has been introduced to everyone, Peach (the starfish) says, "We have got a live one", the first time her face is pressed against the glass so no one can hear her. But in the next shot when she says "Root canal, and by the looks of those X-rays, it's not going to be pretty." her face is pressed against the glass again and everyone seems to hear her.
Factual errors: Mr. Ray is not a Mr. at all, as he lacks claspers (the male reproductive organs found on rays and sharks.)