In substance, that’s what’s wrong (6)

I believe the answer is:

matter

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'in substance' is the definition.
'matter' can be an answer for 'substance' (synonyms). I am not certain of the 'in' bit.

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

Can you help me to learn more?

(Other definitions for matter that I've seen before include "Stuff - mean something" , "Substance as opposed to spirit" , "Affair; be important" , "Subject; be important" , "Carry weight" .)

I've seen this clue in the Evening Standard.

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