I have pushed a branch for this issue to my cpython fork:

https://github.com/JDLH/cpython/tree/bpo-29562_failing_test_getgroups_on_os_x

It modifies test_getgroups in test_posix.py to give better diagnostics in the event of a test failure. It says specifically which groups were in id -G, and posix.getgroups(), but not in the other.

% ./python.exe -m unittest -v test.test_posix.PosixTester.test_getgroups 
test_getgroups (test.test_posix.PosixTester) ... FAIL

======================================================================
FAIL: test_getgroups (test.test_posix.PosixTester)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/Users/jdlh/workspace/cpython/Lib/test/test_posix.py", line 841, in test_getgroups
    self.assertEqual(len(symdiff), 0, msg)
AssertionError: 2 != 0 : id -G and posix.groups() should have zero difference.
Groups in id -G but not posix.groups(): [(701, 'com.apple.sharepoint.group.1'), (398, 'com.apple.access_screensharing')]
Groups in posix.groups() but not id -G: []
(Effective GID (20) was disregarded.)

----------------------------------------------------------------------
Ran 1 test in 0.020s

I don't think this branch is ready yet to submit to the main codebase, but it may help people diagnose the issue.