Maybe a known bug, but I couldn't find anything else in the tree for it.
When the install phase creates hardlinks and the package have preserves them into the tarball correctly, the qmerge phase does not seem to preserve them when copying onto the filesystem.
dev-util/git shows it up for /usr/bin/git-* (in 1.5) or /usr/libexec/git-core/git-* (in 1.6).
It will work just fine if $PORTAGE_TMPDIR is on the the same file system as $ROOT. Otherwise, yes, it's a known issue that needs fixing.
Yeah, I have $PORTAGE_TMPDIR as tmpfs.
For dev-util/git, this hardlink bug costs 70MiB of disk. I'm going to look and see if I can convert the package to symlinks instead for now.
*** Bug 247922 has been marked as a duplicate of this bug. ***
This is fixed in 2.1.6_rc2.