Factual error: Jacques the cleaner shrimp is in a lot of trouble. He is sharing an aquarium with Bloat, a long-spined porcupine fish. Shrimp and other crustaceans are their favourite food.
Suggested correction: Suspension of disbelief. Sharks eat fish, and don't try to rehabilitate themselves to not eating fish. Besides I'm sure the others would have convinced Bloat not to eat Jacques.
Continuity mistake: Towards the middle of the movie, we see a shot with Nemo staring out of the tank, depressed. The camera slowly pans toward the side of the tank and Nemo is reflected in the glass twice. However, towards the end of the movie when Nemo is playing dead, all the fish swim to the other side of the tank and Bloat says something like, "What's happening? Why is he playing dead?" The camera pans to the side of the tank again, but the fish are only reflected once this time. They should have been reflected twice.
Suggested correction: The camera does not pan to the side of the tank, nor do the fish swim past the edge of the glass. The submitter might have confused the black cord that's outside of the tank as the edge of the glass. The view of the fish is correct.
Factual error: After Nigel returns Marlin and Dory to the ocean it is raining and the sky is nearly solid with gray clouds. As Marlin and Dory speak bright sunlight is streaming down through the water all around them, illuminating the ocean floor. Even if the water is extremely shallow where they are swimming the overcast sky would not provide such bright, consistent light. (01:21:45 - 01:22:40)
Continuity mistake: As the fishing net is being pulled up, a fisherman is shown to the left of two wires on the boat leaning on his elbow. Then in the very next shot, the fisherman is in between the two wires, and now he is leaning on his hand.
Suggested correction: He isn't between the wires.
Even if he isn't exactly between the wires in the next shot, he still moves between shots, so the mistake is valid.
Continuity mistake: When Marlin and Coral check on the eggs in the nest, when they first look, no eggs can be seen at the mouth of the cave but a couple of shots later the eggs appear.
Suggested correction: The reason the eggs appear is that the camera may have moved downwards, thus closer to the eggs that would have been at the bottom of the hollow. If it was more upwards, as in the first shot, the eggs would have been below the camera's view.
The camera doesn't move down, it zooms out. There are eggs at the mouth of the cave in the second shot, and in the first shot, the same area of the cave is shown, but there are no eggs visible. The different shot sizes don't matter here.
Plot hole: When Nemo swims off to the boat, a diver pops up and catches him, and all the fish react. But this diver should have been visible to Marlin and co. long before it reaches Nemo, as they are far enough from the boat and looking out into open sea, yet none of them reacts until the diver is right behind him. Also, bubbles should have risen into shot before the diver does. (00:14:25)
Suggested correction: The fish were focused on the boat, not on divers that were toward the bottom of the ledge that they were at.
Audio problem: When Marlin and Dory swim into the deepest part of the ocean to reclaim their mask, they see a light (which we know later, belongs to an angler fish). They stop right underneath the light and says "What is it?" but his mouth doesn't match the movements. It looks as though the animators had Albert Brooks (Marlin's voice actor) say a different line than what was animated.