My Illogical Theories
The first scenario is simply lazy coding lol. You could presume that he was just a bad explorer or something since a cavern surrounded by six particularly-placed rocks would probably come to your attention even after small inspection of the route. I believe that the Pokemon world just owns that NPC, since he ain't the brightest tool in the shed.
In the second scenario, I think the comic you presented is not an accurate depiction of what the tree is meant to look like. Logically, the tree would be a lot bigger if it was said to be blocking the way. You could even consider the perspective of the comic's second frame; fences and shrubs are probably a lot taller in real life - is there a point in a fence if you can peer over it, let alone jump over it? Obviously the player's sprite is as tall as the fences and trees in the games, but the developers probably wanted fences and trees to take up as few tiles as possible. It's merely logical to assume that fences and Cut trees in the games are taller.
As for the third scenario, Chandelure is affected by Earthquake because it is vulnerable to Ground-type moves. Game Freak were not thinking about Earthquake specifically when they assigned Chandelure that weakness - it would hurt if Chandelure was hit by a Mud Shot! But as sumwun said, Chandelure has enough ability slots anyway, so Chandelure couldn't get Levitate.
For the fourth scenario, it could be reasonable to assume that Dragonite was not travelling at full speed, however even if it was, the 1556mph figure comes from the games. As sumwun said, the anime and the games really should not be compared as they were made by different people.
Feel free to comment any flaws in my logic, I'm prepared. Kinda.
Hope I helped. :)