What you need to do is to stop focusing on one storyline and just play the rest. It will unlock sooner or later.
The game 'seems' to be sandbox, but is really more adventure like. And the hints are not always completely accurate, since - as you mentioned - sometimes the preconditions are not always clear.
But there is no known progress bug, unless you modified the games somehow and that causes it.
The game is really a VN or often more like a KN, because although it has loads of
freeroams, often the only way to progress is to follow
one single very restricted path. Visit one place out of the correct sequence and the story order flies out the window or you might even get stuck and locked out of progress. The same goes for you if you intentionally try to avoid some of the events. Pretty much all events in this game are meant to be played, all paths to be followed
In season 2 there was one occasion where the player had multiple places on the map unlocked, so he could visit all of them, with at least two places where the story would progress, but only one of them the
correct one.
The first time I made a wrong choice and the story progress went out of order, the characters (Sophie in particular) started talking about things that never happened. Then I actually changed the script myself in a way that locked out the wrong path - just to make sure that it's possible and rather easy to achieve. That particular logical bug was never fixed by Inceton and I'm pretty sure that later on other similar bugs were introduced, so I stopped paying attention to them, just tried to follow the intended path.
By following each update you're less likely to get stuck, but if you try to start a season from the beginning without knowing the order each event was added to the game, you are likely to get stuck somewhere, miss something or play the story out of order.