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.
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.
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.
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.
Suggested correction: It's not THAT cloudy. It's more cloudy on the right side than it is on the left when Nigel's apologizing to Marlin and Dory.