These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
Moral Event Horizon: Mentioned in-universe, by the male main character, in regard to Crimson. At first Crimson appears to be a Manipulative Bastard at worst, with a little bit of foreshadowing that he might actually be an outright villain. Then you get to the earth ruin. In the middle of talking to a demon ghost Crimson shows up, destroys the frightened ghost for no really good reason, then tries to convince the Dungeon Maker to murder Niko, an innocent little boy whose only "crime" is being half witch. The Dungeon Maker explicitly states this is the point where he went from simply distrusting Crimson to outright hating him.
If that's not enough of a Moral Event Horizon for Crimson he gets another really big Kick the Dog moment later in the game, after Revenger is dead and the female character is playable. The female main, wanting to know the truth about Crimson, goes to meet him in the fire ruin. When she arrives he tells her he's going to kill her, even though he doesn't know her at all or have any reason to dislike her, just because it'll make the Dungeon Maker sad.
The Scrappy: Niko is this to some, thanks to his crush on the (male) Dungeon Maker. He's not shy about making it clear how he feels and many fans found his advances to be creepy.
Viewer Gender Confusion: The Professor who works at the magic shop. He's an old man who could be easily mistaken as looking like an old woman, thanks in part to his robes concealing most of his body. It doesn't help that the game rarely uses pronouns like him/her/etc to refer to him.