Crossword Genius

Where to put croutons? Having difficulty (2,3,4)

Ross

I believe the answer is:

in the soup

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'having difficulty' is the definition.
(in the soup means experiencing difficulty)

I don't understand how the remainder of the clue works.

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(Other definitions for in the soup that I've seen before include "having problems" , "amid trouble" , "Position of stock" , "Where noodles might be" , "Experiencing serious difficulties" .)

I've seen this clue in The Times.
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