When Mr. White is in his flying boat, his gloves disappear. They return in the next scene.
When Sam runs out of the Lake of Life, his clothes are only wet up to his knees, despite having been in a part of the lake where the water's surface was higher than his waist.
When Suicune goes back to the Lake of Life, a nearby Sentret has miscolored ears.
In one scene, when Celebi is eating a berry, the blue tip of its left antenna is missing.
In the opening, Ash is shown in his normal clothes when he is receiving Pikachu, instead of his pajamas as depicted in the first episode of the anime.