Problem code
        Query<UserGroup> query = createQuery()
                .field(&quot;_id&quot;).equal(group.getId());
        query.and(query.criteria(&quot;user&quot;).doesNotExist());

        UpdateOperations<UserGroup> ops = getDatastore()
                .createUpdateOperations(UserGroup.class)
                .set(&quot;user&quot;, user);
        update(query, ops);

Solution (Per skot)
        Query<UserGroup> query = createQuery()
                .field(&quot;_id&quot;).equal(group.getId());
        query.and(query.criteria(&quot;user&quot;).doesNotExist());

        UpdateOperations<UserGroup> ops = getDatastore()
                .createUpdateOperations(UserGroup.class)
                .set(&quot;user&quot;, getDatastore().getKey(user));
        update(query, ops);

The user in UserGroup is decorated with @Reference. Instead of the object being set as a DBRef, it used a BasicDBObject which resulted in the exception below.

<b>What version are you using? (Morphia/Driver/MongoDB)</b>
0.99-SNAPSHOT

<b>Please include a stack trace below:</b>
java.lang.RuntimeException: java.lang.ClassCastException: com.mongodb.BasicDBObject cannot be cast to com.mongodb.DBRef
    at com.google.code.morphia.mapping.Mapper.fromDb(Mapper.java:421)
    at com.google.code.morphia.mapping.Mapper.fromDBObject(Mapper.java:265)
    at com.google.code.morphia.query.MorphiaIterator.processItem(MorphiaIterator.java:53)
    at com.google.code.morphia.query.MorphiaIterator.next(MorphiaIterator.java:48)
    at com.google.code.morphia.query.QueryImpl.get(QueryImpl.java:340)
    at com.google.code.morphia.DatastoreImpl.get(DatastoreImpl.java:498)
    at com.google.code.morphia.dao.BasicDAO.get(BasicDAO.java:163)