[@Antarctic Termite]
Supernatural fauna - This is an interesting point of view. I do believe it to be flawed however because of how broad it is. If we would take every "animal" that has a supernatural element to it and place them in the "monster" category, we'd have practically no animals. Cows are supernatural, as are pigs, goats, cats, wolves, bears, crows, doves, swans, rats and a lot of other animals. But is it fair to put them in the same category as dragons, werewolves, minotaurs and yetis?

Cultural influence - This is of course very important, all of the animals I listed above are obviously not supernatural according to the same culture, but different ones. But it also introduces the idea of monster/animal as subjective. According to the people of Madagascar the lemur is a monster, but to a Chinese person it would simply be a monkey, an animal. So far so good, but I feel that there is still a line that separates the subjective monsters of albino whales, bigger versions of known animals (grizzly bear/dire wolf/giant bat) and freaky lemurs from the objective monsters like dragons, werewolves and zombies. 

Bad planning from the author - Yes, I would say that this is at least 95% of the issue. Either the author doesn't even try to, can't or stubbornly won't justify the difference. Simply going with the "natural vs supernatural". But if monsters exist in the world they have to be natural. 
I like where you're going with your last point, that something has changed to introduce the monsters. That they are somehow created or brought to the world from some other plane of existence.