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I'm seeing a python warning in the Log Messages panel when starting QGIS for Linux, but it starts fine so not sure what's affected by it:

@warning:/usr/lib/python2.7/pkgutil.py:186: ImportWarning: Not importing directory '/usr/lib/python2.7/site-packages/mpl_toolkits': missing init.py
file, filename, etc = imp.find_module(subname, path)

traceback: File "<string>", line 1, in <module>
File "/usr/share/qgis/python/qgis/utils.py", line 204, in startPlugin
plugins[packageName] = package.classFactory(iface)
File "/usr/share/qgis/python/plugins/MetaSearch/__init__.py", line 32, in classFactory
from MetaSearch.plugin import MetaSearchPlugin
File "/usr/share/qgis/python/qgis/utils.py", line 454, in import
mod = _builtin_import(name, globals, locals, fromlist, level)
File "/usr/share/qgis/python/plugins/MetaSearch/plugin.py", line 33, in <module>
from MetaSearch.dialogs.maindialog import MetaSearchDialog
File "/usr/share/qgis/python/qgis/utils.py", line 454, in _import
mod = _builtin_import(name, globals, locals, fromlist, level)
File "/usr/share/qgis/python/plugins/MetaSearch/dialogs/maindialog.py", line 45, in <module>
from owslib.csw import CatalogueServiceWeb
File "/usr/share/qgis/python/qgis/utils.py", line 454, in _import
mod = _builtin_import(name, globals, locals, fromlist, level)
File "/usr/share/qgis/python/owslib/csw.py", line 18, in <module>
from owslib import fes
File "/usr/share/qgis/python/qgis/utils.py", line 454, in _import
mod = _builtin_import(name, globals, locals, fromlist, level)
File "/usr/share/qgis/python/owslib/fes.py", line 19, in <module>
from owslib import util
File "/usr/share/qgis/python/qgis/utils.py", line 454, in _import
mod = _builtin_import(name, globals, locals, fromlist, level)
File "/usr/share/qgis/python/owslib/util.py", line 13, in <module>
import pytz
File "/usr/share/qgis/python/qgis/utils.py", line 454, in _import
mod = _builtin_import(name, globals, locals, fromlist, level)
File "/usr/share/qgis/python/pytz/_init__.py", line 29, in <module>
from pkg_resources import resource_stream
File "/usr/share/qgis/python/qgis/utils.py", line 454, in _import
mod = _builtin_import(name, globals, locals, fromlist, level)
File "/usr/lib/python2.7/site-packages/pkg_resources.py", line 2888, in <module>
add_activation_listener(lambda dist: dist.activate())
File "/usr/lib/python2.7/site-packages/pkg_resources.py", line 758, in subscribe
callback(dist)
File "/usr/lib/python2.7/site-packages/pkg_resources.py", line 2888, in <lambda>
add_activation_listener(lambda dist: dist.activate())
File "/usr/lib/python2.7/site-packages/pkg_resources.py", line 2427, in activate
declare_namespace(pkg)
File "/usr/lib/python2.7/site-packages/pkg_resources.py", line 2009, in declare_namespace
_handle_ns(packageName, path_item)
File "/usr/lib/python2.7/site-packages/pkg_resources.py", line 1961, in _handle_ns
loader = importer.find_module(packageName)@

I've got python2-matplotlib 1.3.1 installed.

But that directory exists and there isn't an __init__.py file,
% ls /usr/lib/python2.7/site-packages/mpl_toolkits/
axes_grid axes_grid1 axisartist exceltools.py exceltools.pyc exceltools.pyo gtktools.py gtktools.pyc gtktools.pyo mplot3d

I did find __init__.py in the following places,
% find /usr/lib/python2.7/site-packages/mpl_toolkits -type f -name '*init*.py'
/usr/lib/python2.7/site-packages/mpl_toolkits/axisartist/__init__.py
/usr/lib/python2.7/site-packages/mpl_toolkits/mplot3d/__init__.py
/usr/lib/python2.7/site-packages/mpl_toolkits/axes_grid/__init__.py
/usr/lib/python2.7/site-packages/mpl_toolkits/axes_grid1/__init__.py