Failed to import the site module

Does anyone know why when I try to run a script built using Py2App I get this error?

The script runs fine if I use Alias mode. Once I pack it I get that error as if was trying to load Blender Pythons site-packages? or anything else I don’t understand.

/Applications/blender-2.79-macOS-10.6/ -b /Users/username/Desktop/test2.blend -a
Read prefs: /Users/username/Library/Application Support/Blender/2.79/config/userpref.blend
found bundled python: /Applications/blender-2.79-macOS-10.6/
Failed to import the site module
ImportError: bad magic number in ‘site’: b’\x03\xf3

Does anyone here work with Python and is currently using OSX?