@Chey1 If it's that you feel strange about this man coming and going from your home without ever even having met him, you could just be honest with the guest and explain that it would be nice if she could introduce him to you at some convenient time, just so you don't feel uncomfortable about some man you've never even met coming and going from your home. That seems reasonable to me.
Otherwise, I don't see that their behavior is overstepping any boundary issues-they seem to be quiet and not disturbing you or intruding into your life. They are adults- I don't see why what hours they keep is of any concern, as long as they aren't waking you up.
You could consider yourself lucky that she actaully booked for 2 people, rather than booking for one and sneaking him in, in the middle of the night.