Hey, wait a moment, did you recover some events from the gallery and play from there?
If recover means like maybe hitting triggers for the main story then yes, I remember I went to Dusk and nothing happened. Then I replayed a couple events in the Event Gallery from the main story as well as Aneko and suddenly I went I was sent into the last section of "The Last Crumbs" based off of that.
- Also just remembered that the last Tsukiko event where you approach her with the carrot is not activating either.
If the gallery isn't the fix all I can think of is for the girls is that maybe they are time gated? Cause if you hop in from a new game where 0.89 started. Meeting Mikosh on like Day 10 when the game may think you are still early game is weird though I'm not sure.