Before going into an interview, you should always prepare at least five questions to ask about the position or organization. These should not seek information you could have found yourself through research; in fact, the best questions actually demonstrate how much research you've done: "My understanding is that you merged with Company X six months ago. How is that transition going, and in what ways do you anticipate it would affect my role here?"
Then there is one question I always like to ask at the end, before asking what the next steps are or what the timeline for hiring is. And that is, "Do you have any hesitations about hiring me that I could address?"
This question serves a number of purposes.
One, it shows that you're proactive. You want to get any obstacles out in the open where you can address them, rather than leave wondering whether there's some weakness in your application no one wanted to mention. You come across not as the kind of candidate who silently hopes, "Pick me! Pick me!" but as one who wants to have a two-way conversation about whether this position is a good fit for you.
Two, it leads hiring managers to show you their cards. It's amazing how much information I've learned about my chances of getting the position from asking this one question. On the one hand, you may get the hiring manager that says, "Well, we would really prefer an internal candidate for this position...," cluing you in that you're not on the top of their list. On the other hand, I've had hiring managers not only share that they had no hesitations about me, but also explain that I had qualifications that no other candidates had, something I couldn't have learned any other way and giving me a hint of what to remind them of in my thank-you note.Most importantly, it gives you a chance to respond.
Ideally, you should try to predict ahead of time what objections the hiring manager might have ("You have little experience in this field") and look for opportunities to explain why these are actually assets ("I would come in fresh, without preconceived notions of how things are done.") But sometimes you won't even know that the hiring manager considers something a weakness until you ask, and you then have an opportunity to defend yourself — either explaining why the perceived weakness is actually a benefit, or explaining how you would work to compensate for the weakness.