Agent cut up for bowel problem (6)
I believe the answer is:
polyps
'bowel problem' is the definition.
'agent cut up' is the wordplay.
'agent' becomes 'spy' (spy is a kind of agent).
'cut' becomes 'lop' (lopping is a kind of cutting).
'up' says the letters should be written in reverse (in down clue: letters go upwards).
'spy'+'lop'='spylop'
'spylop' backwards is 'POLYPS'.
'for' acts as a link.
(Other definitions for polyps that I've seen before include "Such as sea anemones" , "Small growths on mucous membrane as in nose" , "sea anemone forms" , "Organisms of which coral is composed" .)