If "Where's the beef?" is asking for substance relating to an issue, "What's your beef?" is asking what substantive issue to have with someone or something.
Related: "Having a beef" with someone or something.
Example: "I don't like that Barbara." "What's your beef with her?" "Nothing - I just don't like her attitude."
In this case, the speaker has not had a personal conflict with Barbara of any substance. It is not that Barbara stole money from the speaker, damaged the speaker's car, or threw a rock into a window at the speaker's house. The annoyance with Barbara is strictly based on superficial issues.
If Barbara had done some tangible wrong to the speaker, this would be the speaker's "beef" with Barbara.
Not Quite So Simple
While the meaning of "something simple" is, well, simple, "not quite so simple" means, in reality, something requiring a detailed explanation. This expression is used to alter the flow of a conversation or, more usually, an article, shifting to an explanation which explains why a question cannot be answered simply and reflexively.
Example: "When faced with a wild bear, what should one do? Scream? Run in panic? It isn't quite that simple. Either of these reactions may trigger the bear's predatory instincts and place the person in greater danger..."
➤ Read more idioms and phrases, English grammar and vocabulary at Basic English Grammar And Vocabulary .
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