In some machines, soft links have been used, so there are two paths point to the same file.
e.g.
In the list of files installed by PIP (pip_sorted.list)
/usr/lib/python2.7/dist-packages/olefile/olefile.py
/usr/lib/python2.7/dist-packages/olefile/__init__.pyc
/usr/lib/python2.7/dist-packages/olefile/olefile.pyc
In the all_files.list:
/lib/live/mount/persistence/mmcblk0p3/rw/usr/lib/python2.7/dist-packages/olefile/__init__.py
/lib/live/mount/persistence/mmcblk0p3/rw/usr/lib/python2.7/dist-packages/olefile/olefile.py
/lib/live/mount/persistence/mmcblk0p3/rw/usr/lib/python2.7/dist-packages/olefile/olefile.pyc
So that, they can not eliminate each other (which they should).