I think about Oblivion and it's NPC scheduling far too often. It feels like the missing piece in otherwise amazing games like Deus Ex MD or Pathologic 2.
I remember MGS V had elements of this. Guards would patrol, be relieved at certain times, there was scheduled transports of prisoners and resources. If you knocked out an entire base of guards at night eventually the morning shift would turn up and start waking them up, putting the base on alert.
I just remembered Shadows of Doubt, I think that's the most recent game with this system that I've played. It has proc gen cities where every citizen has a job and a sometimes spontaneous daily routine. Every few days a citizen will murder another one and leave behind a trail of evidence. It's supposed to hit 1.0 this month as well.
Very raw and buggy in places but in ways that leads to more hilarious outcomes. You hide in a freezing vent waiting for someone to head out to the club for them to apparently decide nah not tonight 2 seconds after leaving the building and catch you in the middle of reading their emails.