Leaves port having trouble aboard ship (5)
I believe the answer is:
sails
'leaves port' is the definition.
'trouble aboard ship' is the wordplay.
'trouble' becomes 'ail' ('ail' can be a synonym of 'trouble'**).
'aboard' means one lot of letters goes inside another.
'ship' becomes 'ss'.
'ail' going inside 'ss' is 'SAILS'.
'having' is the link.
(Other definitions for sails that I've seen before include "Navigates" , "Ship's canvas" , "Goes by sea" .)