Cryptic crossword clue
Bad feeling caused by tip of instrument left in stomach

The most common and most likely answer to this crossword clue is the 5 letter word GUILT

I've seen this crossword clue in Independent
G
U
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T


Buddy explains!

The straight part
We know that "Bad feeling" is the straight/definition part of the clue. The straight part is often a synonym or definition, in this case bad feeling = guilt.
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 GUILT mean?

GUILT noun
  1. Responsibility for wrongdoing.
  2. The state of having been found guilty or admitted guilt in legal proceedings.
  3. The regret of having done wrong.
GUILT verb
  1. To commit offenses; act criminally.
  2. To cause someone to feel guilt, particularly in order to influence their behaviour.

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