Swastika on the train map.

As you noticed, the symbol is not a nazi one, it's "mirrored". It's far more ancient. It is a religious symbol (well the swastika itself was one - a hindu one if I'm not mistaken - before it was infamously used by Hitler and his pals) used in buddhism and, by extension, shintoism which is the main religion in Japan. When you encounter this symbol (called a manji) on a map, it indicates the location of a shrine. Needless to say, some maps are filled with it (for example, try and look at a map of Kyoto).

Interesting fact : two years ago, the japanese authorities considered banishing this symbol from the maps because tourists (mainly american ones) were frequently outraged as they thought it was a celebration of nazism. Fortunately, it didn't happen. Well, tbh, it'd have been pretty stupid and useless since tourists would have seen the symbol at the entrance of each and every shrine...

Hope I answered your question ;)