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That's close, but in the example I mentioned they genuinely screwed up the metaphor they were quoting, and it was this misunderstanding they then passed to the audience as correct. People who have watched Shrek then use the onion quote themselves because they take the film's misquote at face value.
ETA: In Peer Gynt, the title character, a rapist and thief, is walking through a field at the end of his life. He finds an onion and begins to peel it apart looking for its heart, but there's no goodness to be had - nothing at the core but more stinking onion. This is clearly spelled out as a metaphor for his soul.
The writers of Shrek took the first part of this scene (onions have layers!) but forgot the reveal, and so misunderstood it to mean that you shouldn't just judge someone by their harsh outer skin - completely missing the point that the inside is exactly the same.
Edited by SimsKatieCompletely Missing The Point? Analogy Backfire?
Did the Shrek writers take the onion thing from Peer Gynt? It seems to me like they could just as easily have hit on the idea of onions having layers independently, and then failed to think it all the way through.
Edited by thegrenekni3t

This one is more about the audience than the work itself. What is it when people misuse a work or metaphor because they don't understand or just haven't thought about it in any depth. Specifically, I'm thinking about the famous "onions have layers" metaphor Shrek stole from Peer Gynt, but then completely misunderstood as being about having hidden virtue rather than having no soul.
Edited by SimsKatie