Mother has an afterthought by way of complaint (5)
I believe the answer is:
mumps
'way of complaint' is the definition.
'mumps' can be an answer for 'complaint' (mumps is a kind of disease). I am not certain of the 'way of' bit.
'mother has an afterthought' is the wordplay.
'mother' becomes 'mum' (informal term for mother).
'has' means one lot of letters go next to another.
'an afterthought' becomes 'ps' (ps stands for postscript).
'mum'+'ps'='MUMPS'
'by' acts as a link.
Can you help me to learn more?
(Other definitions for mumps that I've seen before include "Infectious disease, making neck glands swell" , "Swelling disease" , "Acute viral disease, often in children" , "Gland-swelling disease" , "Disease once common in children" .)