In the middle of the 4th chapter after she goes in the Subway station at Times Square(lines RNQW), she comes out at Bowery street station(lines JMZ). The thing is there are no lines that go from Times Square to Bowery Street and the two never connect and are not even remotely close.
Actually, it is possible to get from Times Square to The Bowery by subway. First, you get on either the 1, 2(two), or 3 trains at Times Square, go south and transfer at 14th Street to the F Train, which will lead you the Delancey Street-Essex Street Subway station. From there you can transfer to the J, M, or Z trains to your next stop west; Bowery Station.