Clementine will say two different lines when dropping the bottle of water in the restroom, "Oh, shoot!" or "Oh, shit!", depending on if you mentioned the term "shit" to Clementine on Hershel's farm in Episode 1.
After the game skips to 16 months later, Clementine and Christa are in North Carolina known by the license plate shown by the camp fire.
Clementine ends up being threatened by a man who tells her to stay away from his daughter, the exact same demand made to Lee by Larry.
In episode 2, there is a reference to the film Reservoir Dogs (1992), starring Michael Madsen, the voice actor for Carver. The reference is when Carver looks at a chessboard & remarks "white's in trouble." There is a character in Reservoir Dogs named Mr White, whom Madsen often fights with.
In this episode, Clementine has the torn photograph of Lee from "A New Day", and her backpack and drawing of Kenny from "Long Road Ahead".