Reading some articles. It's a bit muddled because it's a viral story from a foreign country. But what I am confident in saying.

Low usage, this station in particular only had 4 trains a day. Three one way, one the other (the service the student took)

Three other stations closed at the same time, on the same line. One of which only had 2 trains stopping.

There is also the way Japanese train routes are run.