Where does the meat in the Pokemon world come from? In the Pokemon world, the Pokemon themselves are like animals in our world. Instead of fish, the lakes are teeming with Goldeen, Magikarp, Horseas, and the occasional sea dragon. The forests of the Pokemon world are filled with Wurmples, Caterpies, and Butterfrees, while our's are filled with spiders, butterflies, monkeys, etc. Meat has made its appearance on the anime several times. Obviously, since there's no real cows or just plain regular animals in the Pokemon world, the meat could only have come from a poor Miltank or a Magikarp (speaking of which, Meowth tried to eat one once in that memorable episode from the anime). That's quite disturbing if you think of it, since apparently Pokemon are taken with higher regard than the animals of our world and they become our companions, and eating a Miltank would probably feel as gross as eating your pet dog.

How Pokemon know their own names. Taxonomy is a completely artificial concept. A cat doesn't know it's a cat and a Raphus cucullatus (a dodo bird just in case you were wondering!) doesn't know it's a such a thing. The vast majority of Pokemon from the anime, rather than making natural animal-like noises, instead just repeat their species name or some variation of that all day long, which makes no sense. Seems to be a biological thing too, since even the baby Pokemon do it! Also how they even say their name over and over again, much less know what their name is, is completely unexplained since a lot of Pokemon physically shouldn't have the capability of maneuvering their tongues, jaws, and mouths in coordination to form words. And not all of them even have a mouth!

Cross breeding. A female, let's say, Nidoran and a male Nidoran mating together and having a baby Nidoran is perfectly logical. But the cross-breeding just makes no sense whatsoever. There should be no way a male Tauros can even mate with a female Mankey and produce an egg (my apologies for any mental scarring that may have resulted from picturing such an idea). Yes, the egg groups exist to make it more sensible, but that would be the real-life equivalent of mammals being able to reproduce with any other mammal, which is disturbing to say the least (humans mating with cows anyone?). Which also brings up a point that if this were real life (which it isn't, but still), species like Kangaskhan (who could only be female) would have died off since the first one. And the fact that apparently Pokemon reproduction can only occur in a daycare (according to the games) doesn't make this any less weirder.

Differentiating between Pokeballs. Everyone in the anime seems to know exactly what Pokemon they're summoning, but all the Pokeballs look exactly the same, so how do they which one to choose?

The 6 Pokemon in your party limit. I don't see why Ash doesn't just get another bag and stuff all his Pokeballs in there so he'd have all his Pokemon close at hand. After all, I'd imagine the reason why the Pokeballs can inexplicably contract and expand by the push of a button is to make them more compact and easy to carry around.

Why the world hasn't been reduced to oblivion yet. If Pokemon existed in the real world, the world would have been destroyed and reduced to rubble a long, long time ago. Even the weakest ones can spit fire from their mouth or summon electricity from their cheeks. The stronger ones can create tidal waves at will, draw up an electrical storm, cause earthquakes, blizzards, and who knows what else. After all that, nuclear war doesn't seem so bad. The world wouldn't have stood a chance against a planetful of creatures where such godly power was so easily accessible, much less humans, who seem to not only be coexisting with these magical beasts just fine, but also owning them as pets and ordering them around. If anything, it should be the other way around.

Storing in PCs. The whole concept of storing Pokemon in computers completely throws off the entire... organicness (I suppose you can say) of Pokemon themselves, and begs the question, are Pokemon actually just bytes of information? There's no other explanation for the ability to store and transfer Pokemon in your computer as easily as plugging in a USB drive than the fact that Pokemon are no more than bits of data. Not to mention the fact that storing Pokemon in PCs seems to put them in some sort of limbo: they're not living, eating, sleeping, breathing; they're just there. That sounds pretty horrible if you think about it. If I were Ash, I would just put them in a zoo somewhere.

How the Pokemon know when to come out of the Pokeball (or how the Pokeball knows when to unleash the Pokemon). In their perspective, what's the difference between a purposeful throw in the midst of battle versus simply throwing a Pokeball against the wall just for the hell of it?

Where the Pokeball goes after the Pokemon gets called out. A lot of times in the anime, a trainer just throws the Pokeball from a floating hot air balloon or something, a Pokemon comes out, and nothing is said ever again about what happens to the Pokeball. Logically, it'd get hopelessly lost after it crashes down to the earth, to be found by another wandering trainer (maybe that explains all the random Pokeballs you find lying around in the games! :p). However, it just seems to vanish into thin air and reappear conveniently back in the trainer's hand.

The infamous, one-way ledges. Why you can jump over the ledges on one side and can't from the other side in the games remains to be a mystery.

Almost no Bug type Pokemon can learn Fly. This mostly applies to the dual Bug/Flying types, like Beedrill, Ledian, Ninjask, etc. Even non-Flying Bug types like Heracross can technically fly. Seems as if the move is only reserved for "flapping" things birds and dragons.