I was searching around on the web and found this article:
Benedetto secures Bronx–Harlem express bus stop
Your voice has been heard.
“For too long, Bronx residents have been inconvenienced. After speaking with members of the community and learning about their need for an express bus stop in Harlem, I fought to make it happen. No longer will people need to transfer at Mid-town Manhattan to get to their jobs, family or friends.”
— Assemblyman Michael Benedetto
Source: http://assembly.state.ny.us/member_files/082/20060509/
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This certainly explains why some Bronx express buses stop where they do. I always thought that the Bronx express buses that stopped at 125th street stopped there automatically, but they stop there because there are enough residents from these Bronx express bus lines that need that stop.