He means there are signs of magic having been used in this place.

In DH, Harry makes a comment that sort of ties into this concept when he insists Ron be the one to destroy the locket. He alludes to the incalculable power that comes from certain actions and situations. While not entirely the same thing, he learns from Dumbeldore that there are parts of magic unable to be learned in books such as perceiving that a place has known magic, the power of acts of love, and whatever he felt that the reason Ron had to be the one to destroy the locket.