Shortcoming in desert? (6)
I believe the answer is:
defect
I believe this clue is a double definition.
'shortcoming' is the first definition.
(thesaurus)
'desert?' is the second definition.
('defect' can be a synonym of 'desert')
'in' acts as a link.
(Other definitions for defect that I've seen before include "Imperfection - go over to the enemy" , "Lack" , "Deficiency" , "Abandon one's country in favour of an opposing one" , "Fault - default" .)