it happens mostly when something on their sidestory wouldnt make sense if it happens too soon. like if your character does something that they havent yet learnt to do
Spoilers
like on liz's sidestory when mc shapeshifts one of the guys that kidnapped her into a ball of flesh, ella teaches you to do that on the main story and it doesnt make much sense to be able to do that if you only focused on liz's story and did it all early in the game, then suddenly your character went from being able to melt people in the sidestory to struggling to shapeshift a grape's color to red in the main story(solution: do something else till they show up again)