Difficulties putting horse in ship (5)
I believe the answer is:
snags
'difficulties' is the definition.
(snag is a kind of difficulty)
'horse in ship' is the wordplay.
'horse' becomes 'nag' (term for an old horse).
'in' indicates putting letters inside.
'ship' becomes 'SS' (prefix in ship names eg SS Great Britain).
'nag' put into 'ss' is 'SNAGS'.
'putting' is the link.
(Other definitions for snags that I've seen before include "Unforeseen obstacles" , "Drawbacks" , "Hitches" , "Problems" , "Unexpected obstacles" .)