TL;DR: GitHub applied for a US trademark 5 years before the Git project did, so the initial application from the Git project was denied as confusingly similar to GitHub. Rather than litigate who got to use what, the parties came to an agreement to continue using the marks in parallel as they had been doing, which allowed the Git project to be granted a US trademark. The Git project also grandfathered in others who had been operating in good faith like GitLab.
TL;DR: GitHub applied for a US trademark 5 years before the Git project did, so the initial application from the Git project was denied as confusingly similar to GitHub. Rather than litigate who got to use what, the parties came to an agreement to continue using the marks in parallel as they had been doing, which allowed the Git project to be granted a US trademark. The Git project also grandfathered in others who had been operating in good faith like GitLab.
[0] https://public-inbox.org/git/20170202022655.2jwvudhvo4hmueaw...