Difficulty with ship entering sound (6)
I believe the answer is:
hassle
'difficulty' is the definition.
(thesaurus)
'ship entering sound' is the wordplay.
'ship' becomes 'ss'.
'entering' indicates putting letters inside.
'sound' becomes 'hale' ('hale' can be a synonym of 'sound'**).
'ss' going within 'hale' is 'HASSLE'.
'with' acts as a link.
(Other definitions for hassle that I've seen before include "Lashes (anag)" , "Irritating inconvenience" , "Annoy continually" , "Nuisance, bother" , "Pester (colloq.)" .)