Every step of the PhD has new questions, from the first time you read a paper through to the end of your viva. Answers don’t always come immediately. They might take a little time and thought, or during the PhD real, practical research to bring an answer to life. Sometimes there are no answers: you can offer ideas, theories or reasons why no answer comes to mind.
New questions aren’t a problem by the end of the PhD. Questions can be unexpected, but your mechanism for answering – the knowledge, the talent, the skill at thinking things through – is the best it could be.
Any time you get one, a new question is an opportunity for demonstrating what you can do.