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.