Commander beheaded having bypassed constant disorder (5)
I believe the answer is:
ulcer
'disorder' is the definition.
(ulcer is a kind of health problem)
I don't understand how the remainder of the clue works.
Can you help me to learn more?
(Other definitions for ulcer that I've seen before include "Cruel sort of open sore" , "Continuing source of pain" , "Cruel kind of bodily sore" , "Inflamed lesion" , "Cruel sort of body sore" .)