I just played the missions Truth and Reconciliation, Nightfall, Two Betrayals, Sacred Icon, Quarantine Zone, and Midnight; and one of them was not counted towards the challenge Bedtime Stories.
Pretty sure it was one of the last 2 I played, possibly Quarantine Zone because I played it straight after Sacred Icon.
Hey OP, due to the current matchmaking issues 343 have enabled the Peer to peer fallback for MCC, this means that “During this time, some challenges may not be completed and XP grants may not be awarded.”.
You can follow Halo Support on Twitter for further details on when this will be resolved or follow this thread on Waypoint where I am keeping things up to date as info is released: https://www.halowaypoint.com/en-us/forums/85d779d52cfd46918b4f8b638f2e3c7b/topics/known-issue-season-7-update-matchmaking-errors/7e6c2cc6-6e80-4efd-9d24-8ec550019a27/posts?page=1