Gut feeling commanding officer is over defeat mostly (5)
I believe the answer is:
colic
'gut feeling' is the definition.
(pain in one's gut)
'commanding officer is over defeat mostly' is the wordplay.
'commanding officer' becomes 'co'.
'is over' says to put letters next to each other.
'defeat' becomes 'lick' (lick can mean to beat or defeat).
'mostly' means to remove the last letter.
'lick' with its last letter taken off is 'lic'.
'co'+'lic'='COLIC'
(Other definitions for colic that I've seen before include "Abdominal spasm" , "Abdominal pain, especially in infants" , "Early pain" , "suffering" , "Briefly, officer in charge makes a complaint" .)