Using includeKey from a client query, and then saving that object replaces the pointer

My client app is querying a root object and using includeKey to download objects there are pointers to.  The client app then modifies and saves the root object.  After the save, when I inspect my MongoDB one of the pointers has been replaced with the representation of that object.  This then causes errors when that root object is fetched again.  I did not have this issue when using Parse.com.
