Goofs

In the English dubbed version, when Ponyo and Sosuke come across the Devonian-era fish while riding in the toy boat, Ponyo incorrectly calls one of them a Bothriocephalus. The correct name for that specific fish is Bothriolepis. Bothriocephalus is actually the name of a genus of tapeworm.

Near the beginning of the film when Sosuke first puts Ponyo in the green bucket he's just filled with water and asks if she is dead already, she soon would be if the tap water he used was in fact tap water and not sea water.

Salt water fish in a freshwater environment are effectively poisoned and do not survive for long unless they are put back into salt water.