I had the same problem, figured out that it had to do with the order I completed the "Meet Violet" and "Inquire About the Test" missions. Going to meet Violet first prevented the "sigh.. sleep later tonight" event from firing. This led to Lily's story not continuing and leaves the player stuck. Once I went back to an older save and did the "Inquire About the Test" mission first everything went smoothly. Hope this helps, love the game so far!