It is all the foreigners in town for the Rugby World Cup ;) I was in Tokyo this morning (in Oita now for a match). The larger number of foreigners creates chaos out of the order. Really. I intend to make sure I am no where near Tokyo for the Olympics. Shiver.
If you have lived here or spent enough time you get a feel for the rhythm of walking and moving through what to outsiders looks like madness and complexity. However the reality is it is perfectly ordered. One or a few tourist can be absorbed but 1000s just makes it all break!
The consistent line colour-coding and set platform allocations makes it super-easy to find your platform (and train) as a foreigner.
The only issue I ever had was determining the best exit at an unfamiliar station. Pick the wrong one at a larger station and you can find yourself a long way from where you were heading.
Did you try to figure out Shibuya when it was under construction? ;)
Also trust me, it is great you had no issues (engineer likely since you are on HN) and were able to see the patterns, however most foreigners are like deer in headlights.
Also exits are simple. Figure out where you want to be and on their website it will say what station and what exit. Their is alway a map when you get off a platform with the exits labeled.
I was there in May and did end up going in a circle the first time at Shibuya and finding myself back at the viewing area overlooking the crossing after just following the ramps. The stairs down were quite easy to miss.
Once you know to keep walking the platform to the exit you need it's very easy for most stations.
Where I struggled was finding a specific shop or eatery I had previously visited at Ueno. Too many separate concourses and shopping areas.
If you have lived here or spent enough time you get a feel for the rhythm of walking and moving through what to outsiders looks like madness and complexity. However the reality is it is perfectly ordered. One or a few tourist can be absorbed but 1000s just makes it all break!