While the book doesn't explicitly state this as the reason, it's heavily implied. Here's why:
* Lily is constantly on the move: She leaves home, travels with Rosaleen, and walks significant distances during her journey. This physical exertion would naturally lead to sore knees, especially for a young girl.
* Lily's shoes are not ideal: She doesn't have proper walking shoes, and this would further exacerbate the strain on her knees.
* Lily is experiencing a lot of stress: Her emotional turmoil and the difficult situations she faces can also manifest physically, contributing to her sore knees.
It's a subtle detail, but it adds to Lily's characterization. It shows that she's enduring hardship and facing challenges, even on a physical level. Her sore knees are a reminder of her journey and the sacrifices she's making.