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.
The problem is that this doesn't really work in Japan due to the lack of school districts and the the need for teenagers to sit entrance exams for high school. This can see kids going to school in completely different areas to the one that they live in. Their status as childhood friends mean Miharu, Reika and Morita probably all live fairly close to one another, but for everyone else all bets are off.