Not sure if this is a bug , so I'll report it here.
After upgrading to Django 1.7 and running all the migrations, I removed South from the installed apps.
This led to to this error popping up on every migration:
duplicate key value violates unique constraint "auth_permission_content_type_id_codename_key"
It turned out that the table Django_content_type still had a South migrations entry and that this was referenced by a bunch of South permissions in auth_permissions.
I fixed this by removing the content_type and the permission entries. Hopefully this is not happening for everyone that upgrades.