6. Pokemon are energy beings that manipulate physics
It takes a real stick-in-the-muk to demand sound science from a world that contains electric mice, moon creatures, and malevolent balloons. It's usually easier to just cry wizard and move on, but Reddit user nameless88 apparently isn't one for easy answers. In early 2013, nameless noted that the inside of a Pokeball seems to be covered in mirrors, and hypothesized that "the pokemon is converted into light, and then bounces around inside the pokeball at lightspeed... Pokemon possess the ability to convert matter to energy, and the pokeball just exploits this."
That theory led to a landslide of other ideas, each making more sense than the last. Pokemon convert energy into matter, allowing them to manifest fire, stars, giant hands and such for their attacks. Humans and unconscious Pokemon can't be captured with a pokeball, because they can't execute the conversion. Pokemon store energy as they gain experience, and when they evolve, the massive amount they release is converted into their new bodies. Basically, this theory suggests that Pokemon is more scientifically sound than the entirety of The Core.