Result of overindulgence perhaps troubling, Pepys said (9)
I believe the answer is:
dyspepsia
'result of overindulgence perhaps' is the definition.
(dyspepsia is the medical name for digestion)
'troubling pepys said' is the wordplay.
'troubling' indicates an anagram (letters damaged or in trouble).
'pepys'+'said'='pepyssaid'
'pepyssaid' anagrammed gives 'DYSPEPSIA'.
(Other definitions for dyspepsia that I've seen before include "stomach complaint" , "it could result from rushing courses" , "Indigestion" , "It was enough to make any man sick" , "Stomach problem" .)