The Japanese version didn't include the phone conversation with Ash and Dr. Oak at the end of the movie, where Oak hinted that he was Sammy. The producers asked for that sequence to be made.
The Japanese version doesn't include the sequence where Team Rocket is trying to take a peach from a peach tree and eat it. The scene was commissioned by the producers of the English dub.
The phone conversation between Ash and Prof. Oak regarding Suicune is different between the Japanese and the English-dubbed version. The English version altered the scene in order to hint the plot twist at the end. It also removed Tracy and Muk from the scene.