Crossword Genius

Having problems with the croutons there? (2,3,4)

Ross

I believe the answer is:

in the soup

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'having problems' is the definition.
(I've seen this before)

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

Can you help me to learn more?

(Other definitions for in the soup that I've seen before include "Position of stock" , "Noodles may be" , "amid trouble" , "having problems" , "where the stock might end up" .)

I've seen this clue in The Irish Times.
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