Blubbfisch

That's biological not possible. If they see each other only once a year for two weeks she would realize that she's pregnant after this time. and her pregnancy would take part during the time apart. after a year she would old a baby when they meet again.
If they were supposed to be together during her pragnancy they planned for a complete different ending where they spend their hole year together.

The logic holes at the end are bothering me

But what if she gets pregnant?

Okay, but what if she gets pregnant? She won't be able to tell him.
Imagine him coming to their house and seeing a child.

I'm watching the Animation and reading the novel now, after watching this

Well, he is still a teenager with no experience

There are some theories which say that the very last scene showing Seoul and partly smaller becoming screen is a methapher showing that the mains are trying to escape and their world becoming smaller and smaller because they can't hide anymore.
It would be typical for Netflix to make a 2nd Season.