Stink former pupil makes is a mistake (4)
I believe the answer is:
boob
'a mistake' is the definition.
(I know that boob is a type of mistake)
'stink former pupil' is the wordplay.
'stink' becomes 'BO' (body odour).
'former pupil' becomes 'OB' (abbreviation for 'Old Boy' - private school pupil).
'bo'+'ob'='BOOB'
'makes is' acts as a link.
I am not very happy about this link. Some or all of it may be part of another bit of the clue.
Can you help me to learn more?
(Other definitions for boob that I've seen before include "Embarrassing mistake" , "Slip" , "Mistake; breast (sl.)" , "Error" , "Blunder (colloq.)" .)