Most of this has been posted before…
1. In the beginning, the scientists said that they cloned Mewtwo after finding a fossil that was believed to be Mew's. How is this possible that Mew has a fossil? Mew is still alive, and there is also only one Mew in the world. Thus, where did this fossil come from? It can be possible that the fossil can be fossilized fur of Mew, but shouldn't it technically be more of the bone?
2. Not much of a slip-up, but the girl trainer's Dewgong seemed too big. In the TV episodes in which Ash is helping the buff Nurse Joy of the Orange Islands, a Dewgong is about as big as Ash while it plays with him underwater. In the movie, however, the size is incredibly big; since the girl was able to ride on its back.
3. The trainer who owned the Pidgeotto actually did NOT own a Pidgeotto; it was a Pidgeot. Easily defined by the colors and the markings of the "hairline."
4. Not much of a slip-up, but when Ash goes into the water in the fountain after Pikachu has been trapped in the black Pokéball, his hat slips underwater. Yet when he goes up back for air, his hat is still on his head. (But he's holding onto it, so I guess we'll let it go.)
5. Most of the slip-ups occur in the cloning lab underground. When the trainers' Pokemon have all been transferred down, Jessie and James watch the cloning screen with the whole, "Who's that Pokémon?" theme going on. A picture of a Scyther appears and they cry, "Alakazam." However, none of the trainers had an Alakazam. But did anyone have a Scyther, either…?
6. When Pikachu's black Pokéball is about to go threw the cloning process, Ash grabs the ball to save Pikachu. Jessie and James see the Pikachu clone forming, then fuzzing, because Ash has saved his own Pikachu. Later, however, we see a clone Pikachu fighting Ash's Pikachu. But Ash's Pikachu was never cloned! Even if it was, it would technically not be fully cloned, since Ash interrupted the transfusion. So wouldn't the clone Pikachu be deformed, in a way? Or none would exist?
Again, this movie seems to have many slip-ups. Another SLIGHT question (not a slip-up) is who is the mystery of that lady who predicted that the storm was going to be terrible (with the accent)? There is no history about her, except that she was knowledge about storms.