The sequence of major arcs unlocks in order. It's possible to go back to things that you never finished, but not skip over entire arcs -- there are a few arcs that you can miss based on your choices, but they can't be returned to if you do. If you're noticing inconsistencies, it's probably because you started a quest line and never finished it (or the next part just isn't implemented yet) before moving on to another. Or, you might be just reading text for an event that already happened, regardless of how long ago, but those instances should be pretty obvious.
Though, TBH, the story is starting to branch out more, and it's possible the order might be less fixed once more arcs are complete.
Unless you're talking about the Harmonia University arc? That arc certainly doesn't make any sense time-wise, but it never will unless you're actually locked into it, which wouldn't be very fun.