use diferentes alias para la tabla students
y todas las columnas relacionadas
select <Fields to be seleced>
FROM `batches`
INNER JOIN courses ON courses.id = batches.course_id
LEFT OUTER JOIN attendances ON attendances.batch_id = batches.id AND attendances.month_date = '2016-09-05'
LEFT OUTER JOIN students st1 ON st1.id = attendances.student_id AND students.batch_id = batches.id
INNER JOIN students st2 ON batches.id = st2.batch_id
WHERE ('2016-09-05' BETWEEN batches.start_date AND batches.end_date AND batches.is_active = 1 AND batches.is_deleted = 0 AND courses.is_deleted = 0 ) GROUP BY batches.id ORDER BY courses.course_name,batches.id LIMIT 0, 10;