Maybe something is being lost in translation, but the article starts with:

"The train makes only two stops—one when a lone high-school student leaves for school and the other when she returns."

The train makes two stops, rather than "the train stops here only twice". Both may be true, but the initial statement describes actions of the train rather than the station.

Looks like they changed it:

"The train stops there only twice a day—once to pick up the girl and again to drop her off after the school day is over."

It's not the only stop, or even the last stop of the train, at least as it looks on google maps. It's just a poorly worded statement I think.

https://goo.gl/maps/cqZBrzvjJJk

That's definitely mistranslated. It's the station that only has two times of the day when the train stops there.