Every now and then, penalty causes upset (3)
I believe the answer is:
eat
'upset' is the definition.
(eat can mean to upset or distress)
'every now and then penalty' is the wordplay.
'every now and then' indicates alternate letters (letters selected at regular intervals).
The alternate letters of 'penalty' are 'EAT'.
'causes' is the link.
(Other definitions for eat that I've seen before include "Partake of" , "Use a knife and fork" , "and 27: Be humiliated" , "tolerate in diet" , "Scoff" .)