Грешка #1066 - Не е уникална таблица/псевдоним в MySQL

използвайте различни псевдоними за таблицата students и всички свързани колони

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;