Ear nose and throat unaligned and in a mess (9)
I believe the answer is:
entangled
'in a mess' is the definition.
'ear nose and throat unaligned' is the wordplay.
'ear nose and throat' becomes 'ent' (medical abbreviation).
'unaligned' becomes 'angled'.
'ent'+'angled'='ENTANGLED'
'and' is the link.
(Other definitions for entangled that I've seen before include "Confusedly twisted" , "Involved in complications" , "caught" , "snarled up" , "Intertwined; entrapped" .)