Harsh military command may make one uncomfortable (3,2,4)
I believe the answer is:
ill at ease
'one uncomfortable' is the definition.
(being ill at ease is being uncomfortable or uneasy)
'harsh military command' is the wordplay.
'harsh' becomes 'ill' (I've seen this in another clue).
'military command' becomes 'at ease' (I've seen this in another clue).
'ill'+'atease'='ILL-AT-EASE'
'may make' acts as a link.
(Other definitions for ill at ease that I've seen before include "Fidgety" , "appear uncomfortable" , "Unsure and constrained in manner" , "awkward" , "Nervous, uncomfortable" .)