It seems to be vendor's issue not CPython itself. This same issue also happens in Ubuntu 16.10's Python 3.6. Raise any exception can cause this:

Python 3.6.0b2 (default, Oct 11 2016, 05:27:10) 
[GCC 6.2.0 20161005] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> raise Exception
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
Exception
Error in sys.excepthook:
Traceback (most recent call last):
  File "/usr/lib/python3/dist-packages/apport_python_hook.py", line 63, in apport_excepthook
    from apport.fileutils import likely_packaged, get_recent_crashes
  File "/usr/lib/python3/dist-packages/apport/__init__.py", line 5, in <module>
    from apport.report import Report
  File "/usr/lib/python3/dist-packages/apport/report.py", line 30, in <module>
    import apport.fileutils
  File "/usr/lib/python3/dist-packages/apport/fileutils.py", line 23, in <module>
    from apport.packaging_impl import impl as packaging
  File "/usr/lib/python3/dist-packages/apport/packaging_impl.py", line 23, in <module>
    import apt
  File "/usr/lib/python3/dist-packages/apt/__init__.py", line 23, in <module>
    import apt_pkg
ModuleNotFoundError: No module named 'apt_pkg'

Original exception was:
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
Exception
>>> 

Also see https://bugs.launchpad.net/ubuntu/+source/python3.6/+bug/1631367.