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.
Les Yay: 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.
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.
Between Tink referring to him as her best friend and the other dust fairies making fun of Terrence's crush on her, I'd say there's definitely enough there. Not to mention, it's the closest thing the fandom has to a legitimate romance.
In the first movie, Tink attempts to be something other than a tinker fairy, and it fails. In the books, there are fairies whose talents lie in various menial tasks. Now put the two together, and you get something akin to "you shouldn't try to rise above your station, because you're just doomed to fail."
To be fair, in the first movie Tinker Bell goes ahead and invents machines that, if you think about it, render the other Fairies' Elemental Powers obsolete. The films doesn't really explore this, but it's something.
Ignoring the books doesn't help either: The line "Remember who you really are" is too easy to change into "remember who we say you are, because there's no way to change your life." Apparently the fairies don't believe that practicing with passion can be better than having a natural talent that you don't enjoy.
The third movie has a surprisingly Anvilicious "Science Is Bad, Science Is Wrong", and Scientists Hate Imagination (What?) But everything will be great if you don't ask questions and just believe!" Arguable though, in the girl also uses surprisingly scientific methods when locating a real fairy.
In Pixie Hollow Games, Rosetta is shamed for being a Girly Girl and being afraid of getting dirty in the games. While the message may be that you can be girly and still do well at sports, the structure of the story could also give the impression that you can't be both, as Rosetta has to get filthy in order to redeem herself in the eyes of her friends.
And about those incomplete fairies that everyone dreads being...they're the fairy equivalent of naturally disabled people.