Indigestion, said Pepys, is troublesome (9)
I believe the answer is:
dyspepsia
'indigestion' is the definition.
(I know that indigestion can be written as dyspepsia)
'said pepys is troublesome' is the wordplay.
'is troublesome' indicates anagramming the letters.
'said'+'pepys'='saidpepys'
'saidpepys' anagrammed gives 'DYSPEPSIA'.
(Other definitions for dyspepsia that I've seen before include "Heartburn" , "Stomach problem" , ""It gives me wind problem"" , "Stomach upset - spied a spy (anag)" , "stomach complaint" .)