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Japan is one of the most densely populated countries. While Kyoto is not a huge city, it is still a city. How the hell do these dozen or so teenagers run into each other everywhere they go as the plot demands?
See also every school anime ever. For what it's worth, if they're all going to school together, it's reasonable to assume they live close to their school and thus to each other, so they would tend to travel in a lot of the same areas just due to geography.