Several quests can accelerate or halt the speed of in-game time, all of the prologue quests up-to the first encounter with a Volatile at night will have the day/night cycle advance based on milestones rather than minutes:
Seeing the airdrop, opening the empty airdrop, the first encounter with Rais' goons and burning the Antizin. Time progression will halt or accelerate based on proximity to the the next stage of the quest.
Likewise, the first time entering Old Town will consistently start at dusk, as will the destruction of the apartment and the
kidnapping of Jade
During the events of these quests time may accelerate to meet the requirements of these quests, and that may be what you're seeing. I don't think any of the side quests force the time of day to change, but about one third to one half of the main quests will.
Other reasons time may change include an attack from the monster in Be The Zombie, which will always, instantly, set the time to midnight (+/- one hour). This is too abrupt for what you're referring to, though.
Lastly, joining a Co-op game will set you time to your host's time. It's possible that your time was similar enough to the host's time that it looked like natural temporal progression than the instantaneous jump it actually is.