The most common and most likely answer to this crossword clue is the 9 letter word QUEERNESS
I've seen this crossword clue in The Times
Q
U
E
E
R
N
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S
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Buddy explains!

The straight part
We know that "vaguely unwell feeling?" is the straight/definition part of the clue. The straight part is often a synonym or definition, in this case vaguely unwell feeling? = queerness.The cryptic/wordplay part
In cryptic crossword there's often an wordplay/cryptic part as well.This part involves a more complex hint, such as an anagram, homophone, hidden word, etc.
Sadly, We don't have an explanation for this specific crossword clue yet.
What does QUEERNESS mean?
QUEERNESS noun- The quality of being queer or odd.
- Something queer; an oddity.
- The quality of being queer, in the sense of not conforming to sexual or gender norms.