Trouble — that's in the soup! (3,5)
I believe the answer is:
hot water
This clue is a double definition.
'trouble' is the first definition.
(to get in hot water is to get in trouble)
'that's in the soup' is the second definition.
(a soup might contain hot water)
(Other definitions for hot water that I've seen before include "Bed warmer" , "Taps contents" , "(Wet?) trouble" , "This could mean trouble!" , "Difficulty" .)