I recently rewatched this movie, and something came to mind that I never really noticed or thought of before. I don't think it's been bought up here before, so here goes.
Having just overcome the Storm of Preventional Access and being guided by zombie Joy into Mewtwo's arena, Misty makes the decision that Togepi might not enjoy the environment they're in and places Togepi in her bag, zipping it up. Upon which a plothole emerges.
Togepi didn't reappear during the entire movie. Not only was it locked in a small space and struggling for air, it got thrown around during the running and jumping Misty did throughout the film. And when the clone balls started catching all the active pokemon, not one started colliding with Misty's bag. Either the bag was bulletproof, or another situation arose.
Togepi wasn't around anymore. Of course Togepi was alive and well when the trio are placed back at the Pokemon Centre, so Mewtwo may have revived it somehow. In any case Togepi's position is rather odd.