For posterity's sake:
Within the scope of MU3 requirements we certified the ability to generate CCD documents by virtue of operations on Binary  and DocumentReference . Ability to retrieve general clinical documentation is not included within the scope of MU3 certified technology. So, the issue you are running into now is that the client system is configured to meet the requirements of MU3 certified technology, but it is not configured to support the general document query. This will likely occur at other client sites as well as you continue rolling out your app, so we would like to request that you disable the query for general clinical documentation.
Feel free to use the operations on either Binary or DocumentReference to generate CCD if that is something that would be valuable for your end users.