I wouldn't say it comes naturally. It comes from noticing points of confusion in the world and making an effort to ask the big Why? question.

And then refining your question to arrive at a different question, which may be a better question.

E.g. Why is my father in law so difficult to get along with -> Is my father in law difficult to get along with? Well, he gets along just fine with others... -> Why is it so hard for my father in law to get along with me? What is different about our dynamic?

One question leads you to the next, but you have to put some effort into the process.

An excellent book on the topic: A More Beautiful Question https://www.amazon.com/More-Beautiful-Question-Inquiry-Break...

"A More Beautiful Question: The Power of Inquiry to Spark Breakthrough Ideas"

It's a very insightful read on how you can see the world differently by simply asking questions (even if you never get an answer)

https://www.amazon.com/More-Beautiful-Question-Inquiry-Break...