Difficulties putting horse in ship (5)
I believe the answer is:
snags
'difficulties' is the definition.
(I know this)
'horse in ship' is the wordplay.
'horse' becomes 'nag' (term for an old horse).
'in' is an insertion indicator.
'ship' becomes 'SS' (prefix in ship names eg SS Great Britain).
'nag' inserted inside 'ss' is 'SNAGS'.
'putting' is the link.
(Other definitions for snags that I've seen before include "Unforeseen obstacles" , "Drawbacks" , "Hitches" , "Problems" , "Unexpected obstacles" .)