Anime (and manga, of course) can be so heavily stylized that a lot of fans end up forming a fantasy version of Japan in their heads that doesn’t square with reality. They get some really odd ideas sometimes, and that results in a weird form of culture shock when they visit.
This said, many things you see featured in these stories are true and very common in Japan. I found an interesting post on Quora listing some of them.
What anime tropes often hold true in Japanese culture?
Kids walking alone, or in pairs, or a small group, to school is real in Japan. [When going to school in the morning, elementary-school children living in the same neighborhood gather at the same spot every day and walk to school together in a group] The running with toast in their mouth is not. The red bookbags are also real, though they actually come in a rainbow of colors.
Cicadas in any summer scene is real.
Catching them along with other bugs is real to an extent.
Scooping and throwing water on the front steps of a store, or home, or tombstone is real. It’s called Uchimizu. Traditionally a bucket and scoop are used, but lately hoses have become more common. This is mainly a summer tradition.
The tombstone one is used to both clean the grave and to make sure the deceased do not go thirsty in the afterlife.
Calling an upperclassman at school or senior at a company “Sempai” is true.
School uniforms are real but only for government owned and private schools are they required.
Most Japanese homes (not apartments for the most part) have at least one traditional room with tatami mats. This is mainly true for homes built before 1995. In 1995 building codes were changed in Japan to allow houses to be built without one of these rooms if so wanted.
Love Hotels are real, and they are everywhere.
Hot springs and public baths are real, along with the separation of the sexes in these facilities. And while there are mixed hot springs in Japan, they are VERY rare.
Clubs in Japanese schools are also real.
Country schools will have an old school building still standing (usually somewhere outback). True! Schools located in more rural districts will have an old school building that was used it the past, still standing on their property and still being used. Many for storage or for club use or as a backup school building in case something happens to the main school building. They are also used a emergency shelters as was the case in 2011 after the earthquake.
Crams school are very real in Japan. [Unfortunately]