First, some of the stories conect weirdly,
This is not the final version of the game. It may be it is not possible in this state of the game to completely prevent events connecting weirdly when some planned events are not yet in the game.
The game has a lot of content and side plots with many characters. It does get very complicated when what happens with one character affects the event of another character. Making sure the events can not happen in wrong order takes a lot of work.