The two families being spoken of here are the Musgroves at the Great House and Charles and Mary at the Cottage, not the Elliots of Kellynch and Charles/Mary.

The paragraph just before spoke of the two Uppercross homes, and then says that Anne knew the ways of Uppercross as well as Kellynch. Remember that Kellynch and Uppercross are three miles apart, and so they will not be just dropping by at all hours with no notice or on a whim. Anne just came from Kellynch, and so would not have expected anyone from Kellynch to be with Mary; she was surprised that no one from the Great House (Louisa or Henrietta) was there.

"Here Anne had often been staying. She knew the ways of Uppercross as well as those of Kellynch. The two families were so continually meeting, so much in the habit of running in and out of each other's house at all hours, that it was rather a surprise to her to find Mary alone; (ch 5)