- In the series finale, instead of sending Rusty to the past to talk his past self into staying with his father's deli, why didn't Julian, the EV trainer, send himself back to the "How to Breed a Perfect Pokemon" episode, and talk his past self out of helping Rusty create the perfect Bidoof?
- Peanut Butter's murder of Agatha is a perfect example of what befell the trainers that opposed him, even moreso during his world conquest. Since Peanut Butter wouldn't harm his fellow Pokémon, his obvious target would be the human trainers that enslaved them. However, what would Peanut Butter have done to the Pokémon who were genuinely loyal to their masters?
Headscratchers / Pokémon Rusty