Some trouble – but only some – for transport system (5)
I believe the answer is:
metro
'for transport system' is the definition.
(I've seen this before)
'some trouble but only some' is the wordplay.
'only some' says the answer is hidden in the clue.
'METRO' is hidden in the letters of 'some trouble but'.
(Other definitions for metro that I've seen before include "The Paris Underground transport system" , "Paris underground rail system" , "what moves many Parisians" , "Parisian underground system" , "French underground" .)