Continuity mistake: In the scene where Lisa feeds Ponyo and Sosuke noodles some of them fall on the table. However the noodles disappear and reappear between shots.
Factual error: Sosuke rescues Ponyo from the sea, and then puts her in a bucket of tap water. Fresh water would kill a saltwater fish.
Other mistake: After the flood, Ponyo uses her magic to enlarge the ship along with all its accessories. At the end of the journey, Ponyo loses her magical powers and the ship shrinks back along with all the ship's accessories. A captain's hat is among the shrunk accessories, although Sosuke used it from the beginning of the film and it was always adult human size.