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.
YMMV: Disney Fairies
Designated Villain: Almost always Vidia, though less so in The Great Fairy Rescue, and Ginger in Dulcie's Taste of Magic.
Fan-Preferred Couple: It would appear that Terrence was supposed to be Tink's love interest, but a significant portion of the fandom thought he was a pretty boy caricature, and thought that Tink/Bobble was much more appealing.
Silvermist, the water-talent fairy seems pretty into Tinker Bell. Or at least more affectionate than is "proper" for two platonic fairies! She greets Tink by stroking her nose and saying, "Easy...Silvermist's got ya."
If we're going to get into Les Yay for this fandom, that's hardly the most prominent example... the high ratio of female characters does increase the possibilities.
Of course it doesn't help that the twos relationship is played as and compared to Star-Crossed Lovers.
Moral Event Horizon: In Pixie Hollow Games, Rumble crosses this when he shoots Rosetta and Chloe's racecar with a lightning bolt. Certainly, it's a horizon crossing in the eyes of his partner, who reacts by throwing the race.
Nightmare Fuel: In Great Fairy Rescue, Vidia and Tink's reactions to the butterflies that were on display in the human's household. Considering the fact that in the films, they've shown that the insects are all personified and the live butterfly in the jar that Elizabeth's father caught has cartoonish eyes, its mildly shocking to see them dead and on display.
Older Than They Think: The word "fairy" was used in JM Barrie's original Peter Pan. The word "pixie" was used in Disney's film for no apparent reason. So please don't whine because they use the word "fairy" in this adaptation.
Some people find the idea of mouse milk and cheese disgusting.
The weird Ship Tease that came up between Captain Zerina, a fairy, and her first mate, who is a human adult male. He came across as lovingly admirable of her abilities, even wistful of her, and he was the only one who understood anything she said. Zerina was clearly happiest with him and was the most fond of him. Then he stabs her in the back and you learn for certain that he's Captain Hook.