The different stories are happening in the same range of days, but technically, if you choose to hang out with Jun instead of Shoichi, the event with Shoichi won't happen, leading to the MC forgetting about something important to Shoichi for example, so...
Yeah, it's something that happens regularly with a lot of the character throughout the game, I guess it's just some mistakes, wrong file selections, and things like that, it will probably get fixed in future updates, though, it's a good idea to say when it happens in game, so it's easier to fix.
You can't find this info anywhere, it's not clear if any of the characters are bi or gay, maybe we will know in the future, for now, it's just theories.