Pain is in a subtle difference (8)
I believe the answer is:
nuisance
'pain' is the definition.
('nuisance' can be a synonym of 'pain')
'is in a subtle difference' is the wordplay.
'in' indicates putting letters inside.
'a subtle difference' becomes 'nuance' (I've seen this before).
'is' put inside 'nuance' is 'NUISANCE'.
(Other definitions for nuisance that I've seen before include "Trouble" , "Pest, source of annoyance" , "Source of irritation, person or thing" , "'Pest, annoyance (8)'" , "Annoying person/thing" .)