With second thoughts mother has a complaint (5)
I believe the answer is:
mumps
'a complaint' is the definition.
(mumps is a kind of health problem)
'with second thoughts mother' is the wordplay.
I cannot really see how this works, but
'second' could be 's' (common abbreviation) and 's' is found in the answer.
'mother' could be 'mum' (informal term for mother) and 'mum' is found within the answer.
A single letter 'p' remains which might be clued in a way I don't understand.
This may be the basis of the clue (or it may be nonsense).
'has' acts as a link.
Can you help me to learn more?
(Other definitions for mumps that I've seen before include "Viral disease with swellings" , "Parotid gland disease" , "Epidemic parotitis" , "Swollen-face disease" , "Virus disease causing painful swellings in neck" .)