At first, she thinks that something about what she's said has upset him, but then it seems that he's tripping over the magic bit, despite the fact that he's well aware of magic existing. That's a bit confusing, since she can't imagine anyone believing that magic simply appeared one day without it having been there all along.

"Well... there's always been magic," she points out, frowning a little. "I don't know who this 'Traveler' is, but magic is a primal force of nature. Even the people who were born without it and who think it's only fiction know what it is, even if they don't believe in it. Muggles - people who can't do magic - used to know about witches and wizards, but relations got a bit strained, so the wizarding world retreated into its own secret communities around the world and made it so that most Muggles believe that magic is little more than a myth. That may be why there are no widely-known records of magic having existed during my time."

But the wizarding world keeps records of its history, as she's learned from the History of Magic classes that had seemed to drag on even for her. That leads Hermione to wonder just what's happened between her time and Mac's that such records would no longer exist, or that they'd be kept locked away.

"What exactly... happened? You make it sound as though Earth as I know it no longer exists, rather than it simply progressed through time."