Select naval vessel, causing difficulty (6)
I believe the answer is:
pickle
'difficulty' is the definition.
(pickle can informally mean a difficult situation)
'select naval vessel' is the wordplay.
'select' becomes 'pick' (picking is a kind of selecting).
'naval vessel' becomes 'le' (I am not sure about this - if you are sure you should give a lot more credence to this answer).
'pick'+'le'='PICKLE'
'causing' acts as a link.
Can you help me to learn more?
(Other definitions for pickle that I've seen before include "A preserved vegetable or a fine mess" , "Marinate" , "Relish for cheese" , "Relish, difficult situation" , "Steep - predicament" .)