Pretty sure it's just different routes messing with eachother. If you progress Charlotte's then she won't be there to ask her about Mia's phone. There is a lot of bugs but if you just stay focused on a single girl you usually won't encounter too many.
Viewing post in My Girlfriend's Friends comments
It's not a bug so much as a dead-end you create for yourself. It literally give you a hint that you need someone who knows the library's environment to help you look for the phone. Charlotte is the only girl who goes to the library, so you need to have talked with her at least ONCE for her to show up there.