Art-Style Dissonance: Though definitely Lighter and Softer in many places than many other Old World of Darkness game lines, the 2nd Edition corebook has a rather infamous example among the fandom depicting a cartoonish bear with a bunch of balloons. Not bad in and of itself but hardly in tune with the themes, mood, and tone the text of the game wishes to portray.
Fridge Horror: Yeah, it's a lighter game then Changeling: The Lost, isn't it? There, you play someone who escaped Mind Rape at the hands of alien gods, while here you're fighting to restore wonder and hope...and will explicitly lose due to metaplot saying so, and you won't live beyond your thirties unless you go Dauntain. Hence, why a lot of players think Lost is actually the more hopeful game.
Fridge Logic: Banality brings about a lot of this. Why, for instance, are scientists Banal, when they are often noted as some of the most imaginative and creative people around in Real Life? Why does growing up rob you of Glamour, when people not suffering clinical depression have been repeatedly noted to retain their dreams and hope throughout life, as noted in psychology?
A lot of this has to do with the game being set in the Old World of Darkness. While each game can be played as their own universe, a lot of the fluff and metaplot do involve the other races. The setting is often dark and depressed, and with the Weaver and various other forces suppressing humanity, dreaming is extremely hard.
Misaimed Fandom: One of the oddest examples of this happening. There is an actual society called the "Otherkin" who believe that they were mythological creatures in previous lives. They thought that so much of the game was spot on that they concluded the makers of the game were in fact changelings themselves. One of the developers of the game went out of their way to deny this.
Scrappy Mechanic: The first edition initially had cantrips be randomly created from a deck of 150 specialty cards, which were sold in randomized collectible boosters.
Squick: The sluagh kith literally thrives on this and players are often encouraged to be as creepy and disgusting as possible in order to gain Glamour. Redcaps have an earned reputation of being brutish cannibals and then you get into the idea that changeling lovers are often reincarnated and emerge from chrysalis in the bodies of children....
That One Rule: More like a set of rules, the game's magic system is notorious even among its supporters for being shall we say...extremely expensive and rather underwhelming.
Specifically the fact that the character's magic is VERY difficult in universe and the character either has to spend all of their Glamour or spend several rounds casting even a single first level spell. Sometimes both. Couple this with the fact that Glamour is extremely hard to acquire unless you want to go full on evil or risk insanity. Harvesting it safely can take months.
Which would be fine if it weren't for the game being specifically about magical creatures doing magical things in the modern world. While this is hardly to the point of a full on Scrappy Mechanic or Grappling with Grappling Rules, it is enough that even enthusiastic players find it...frustrating. Even the game's developers have said that they will address this in the upcoming 20th Anniversary Edition.