Take for example contrib.auth - it defines User, Group and Permission models for you. Frequently this is an issue - what if I don't want a username of 30 characters ? What if I want OpenID authentication instead ?
Sure, you can override this but then you find that a whole lot of 3rd party apps - comments, admin etc - rely on these models, which in turn depend on lower-level functionality such as the ORM or templates. The very fact that you have a framework telling you what your data model should look like just feels "wrong".
Does this mean that you shouldn't use Django ? Absolutely not, there are many projects suited to Django - especially content sites where you are putting together large building blocks with some homemade glue. But I've found it more trouble than worth for smaller projects, or where you have very specific requirements - in these cases (assuming you want to stay in Python) - I'd recommend Flask or Pylons.
Unfortunately Django has become the new Blub framework for Python web development, which means it's used by companies by default, rather than being a useful but limited tool in the toolbox.