If you say 'Good question' in reply to a question, you mean that it is a difficult question to answer, or perhaps that you are embarrassed about the answer or do not know the answer.
[spoken]
'Why didn't you appoint Ron twelve months ago?'—'Good question.'
See full dictionary entry for question
good question in British English
noun
a question that is hard to answer immediately
Examples of 'good question' in a sentence
good question
They are either a good answer to a bad question or a bad answer to a good question.