The link between /usr/bin/git and /Application/Xcode.app/Contents/.../bin/git is hidden.
I don't know how you would discover this: ls indicates /usr/bin/git is a regular file rather than a symlink; stat -f "%i" says the two files have different inodes, so they're not hardlinked.
What is the nature of the link, and how would you find this if you didn't already know?