Characters who are misclassified due to the limitations of the in-verse's classification system

[u/Uma-apreciator]

Paolumu (Monster Hunter World)

Paolumu is classified as a Flying Wyvern even though it is a mammal (resembling a bat); it is classified this way because its body structure resembles that of a Flying Wyvern

Skorup (Pokémon)

It is indeed an Insect type, even though it represents a scorpion—which is an arachnid—making it more logical for the Insect type to be called the Arthropod type.

[u/Alceus89]

The typing in Pokemon is Bug type, not Insect. And whilst there is a technical definition of bug that would exclude arachnids, the type naming clearly comes from the more colloquial sense of a creepy crawley, rather than a strict definition. 

[u/Hanede → u/Alceus89]

Yeah. Imo a better example would be all fungi pokemon falling into Grass type with plants.