Wall-e: That's anthropomorphization. It's not meant to be a realistic depiction of an artificial intelligence, it's more like the talking animals in The Lion King and countless other cartoons.

Rutherford atom: A reasonable hypothesis once, now a simplified analogy. While it may be misleading when taken at face value, it's not worthless as an educational tool as long as you make clear that's an analogy.

Monster and lady: Why are you focusing on the fact that the monster is holding a lady while ignoring the elephant in the room, the gigantic humanoid monster itself? Clearly, again, this is not meant to be a realistic depiction of an alien biological organism, it's meant to be an allegorical depiction of hostile foreigners (monsters that, stereotypically, "steal our women").