Small cake has so upset ship's officer (5)
I believe the answer is:
bosun
'ship's officer' is the definition.
(I've seen this before)
'small cake has so upset' is the wordplay.
'small cake' becomes 'bun' (a bun is a small cake).
'has' indicates putting letters inside.
'upset' shows that the letters should be reversed in order.
'so' in reverse letter order is 'os'.
'bun' going around 'os' is 'BOSUN'.
(Other definitions for bosun that I've seen before include "Crew's foreman" , "Petty officer on a merchant ship" , "Ship's officer in charge of equipment and crew" , "chair for some work on the side" , "who controls crew?" .)