Active record always appending "order by created_at desc"

The error is coming from the :include because your association
doesn't define the table name.
I believe you want your association to look like

    class User
      has_many :notes, :order => "notes.created_at desc"

As far as I know you can't prevent that from scoping all your find
However, in your case the order is the same in the association as the
find, so, who cares.

Side note, this is harder to read but an alternative solution that
stay locked to your note table name if you change it or something

    class User
      has_many :notes, :order => "#{Note.table_name}.created_at desc"