In the scene where they first visit the lake of life, Sam wades into the water (all the way up to his waist). As he steps out there is only water at his ankles and moments later there is no water.
Back when the movie was in the pre-planning stages, the story was supposedly going to revolve around the GS Ball, which Ash and company carried all throughout the Orange Islands and 1/3 of the way through Johto. Evidentally, the GS Ball was going to be finally opened to reveal that Celebi was hidden inside. This may have been the movie's plot had Pokémon Crystal not come out for the GameBoy Color.