Oh, yeah. That scene was intentional, and it'll make sense very soon. If you pick a certain path in Episode 2, you'll learn some more about that, but it's a big part of the main plot.
Thanks! I'm always glad when someone actually cares about the story, not only NSFW content.
I don't know which things don't make sense, but, yeah - everything is connected. I hate plot holes - that's why I'm always careful not to miss anything.
