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: Charlie and the Chocolate Factory
Accidental Innuendo: In one of Dahl's writings for Playboy, "schnozzberry" was used as a euphemism for "penis."
Harsher in Hindsight: Viewers might view the Oompa-Loompas in a different light once they lean about the real life child slavery issue the cocoa industry has.
And the Amusing Injuries the kids suffer are much more terrifying if one remembers that children used to work in factories, and often suffered horrific actual injuries (sometimes fatal) in case of a slightest mistake.
This one's justified, though, in that Wonka didn't save the Oompa-Loompas from primitive living conditions (which was the historical justification of the "white man's burden"), he saved them from the daily fear of being eaten by monsters!
Heartwarming Moments: Grandpa George, a completely irascible curmudgeon who had virtually nothing good to say about anything, tells Charlie, when he offers to sell the golden ticket in order to support the family, that he would be a fool to sell his dream for something as common and ridiculous as money. Considering how cantankerous and irritable he was to that point, it comes out of nowhere that he is the one who speaks out against selling the ticket, particularly in contrast to his stating that Charlie's one bar a year didn't stand a chance in hell of winning in the first place.
Magnificent Bastard: The Oompa-Loompas' 'improvisation' smacks of conspiracy, but ramps it straight into casino territory, as it rather implies that he cherrypicked those kids specifically.
Memetic Molester: Willy Wonka. Beyond the Nightmare Fuel elements of Johnny Depp's performance, when the film hit theaters it was in the wake of Michael Jackson being found not guilty on child molestation charges. As Depp-Wonka and Jackson are superficially similar in appearance, the film was the butt of jokes and questions as to whether this was intentional.
Purity Sue: Charlie, who's a saint in comparison to his alternate universe self (who was still a good kid, but flawed like a regular child). He's hardly even given a chance to test his character for the first half of the film, unlike his 1971 self who faces the temptation of both Slugworth's deal and the fizzy lifting drinks.
This is actually more in line with how he was written in the book. Whether or not staying faithful to the book was a good thing in this case depends on the viewer.
Squick: Augustus Gloop goes for a swim in chocolate intended for eating. A few days later someone in the world will be eating chocolate that a fat boy has been swimming around in for a few minutes....
They Wasted a Perfectly Good Plot: Specifically, it would have been great see to Depp recite the full "We have no way of knowing..." poem with all the manic energy his character used in the book.
Mike Teevee received an update from a television addict obsessed with Westerns to an videogame-playing technology nerd, an image children of the day can better relate to. His flaw is that too much time "gaining intelligence" from TV and playing violent video games has made him a dickish, violent little know-it-all with no imagination. This may be Hypocritical Humor, as some of Tim Burton's works, this one included, have actually gotten video game adaptions (See: The Nightmare Before Christmas). Though it does make the Oompa Loompas still insisting that television was responsible pretty nonsensical.
Likewise, Violet is updated to being overly competitive, rather than merely a gum chewer. The film even lampshades the hypocrisy of Wonka hating gum, when he manufactures and sells the stuff.