Troublesome plant, very small, died (4)
I believe the answer is:
weed
'troublesome plant' is the definition.
(I've seen this before)
'very small died' is the wordplay.
'very small' becomes 'wee' (I've seen this before).
'died' becomes 'd'.
'wee'+'d'='WEED'
(Other definitions for weed that I've seen before include "Useless plant - useless person" , "Hoe to remove it" , "dope" , "gone!" , "Intrusive plant; weak person" .)