DBObject clause1 = new BasicDBObject("scores", new BasicDBObject("$elemMatch", new BasicDBObject("type", "homework").append("score", new BasicDBObject("$gt", 90))));
DBObject clause2 = new BasicDBObject("scores", new BasicDBObject("$elemMatch", new BasicDBObject("type", "exam").append("score", new BasicDBObject("$lt", 50))));
Използвайте го по този начин.