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.
Evil is Cool: Between the Night on Bald Mountain and Ave Maria sections, representing in turn the profane and the sacred. Take a guess which one has burned itself into people's memories the most.
The Firebird from 2000. Make the pun at your own peril.
Unfortunate Implications: Sunflower, the servant centaurette in "The Pastoral Symphony", whose human half looks like a black "pickaninny" and who performs menial tasks for the white-featured centaurettes. Deleted from all releases since 1969, so most modern viewers haven't seen her. If you're curious, there's YouTube (first appearance about 1 minute in).
On a less offensive level, the dancing mushrooms, which are clearly made to resemble old-fashioned Asian caricatures with slit-eyes and those funny cymbal-shaped hats.
Ironically, nobody feels any need to complain about the fish in Nutcracker Suite, the Russian flowers, or even any implications people interpreted from Dance of the Hours.
Vindicated by History: The film was derided by many in its original release as a kitschy travesty, but now is regarded as one of the great masterpieces of Western Animation