Ошибка при получении # 1221 - Неправильное использование UNION и LIMIT

Это вызвано изменением в MySQL 5.7. Чтобы решить эту проблему, вы должны "вложить" свои SELECT, как показано ниже:

SELECT * FROM(


    SELECT t1.TraineeID,
           t2.attnDate,
           MIN(t1.attnTime) AS inTime,
           (CASE WHEN MIN(t1.attnTime) < MAX(t1.attnTime) THEN MAX(t1.attnTime) else '' end) AS outTime,
           (CASE WHEN t5.Slot ='1' AND t1.attnTime<=(SELECT inTime FROM tbl_threshold WHERE id = '1')THEN 'P' 
                 WHEN t5.Slot ='2' AND t1.attnTime<=(SELECT inTime FROM tbl_threshold WHERE id = '2')THEN 'P'
                 WHEN t5.Slot ='3' AND t1.attnTime<=(SELECT inTime FROM tbl_threshold WHERE id = '3')THEN 'P'
                 WHEN t5.Slot ='4' AND t1.attnTime<=(SELECT inTime FROM tbl_threshold WHERE id = '4')THEN 'P'
                 WHEN t5.Slot ='1' AND max(t1.attnTime)<(SELECT outTime FROM tbl_threshold WHERE id = '1')THEN 'Early Out' 
                 WHEN t5.Slot ='2' AND max(t1.attnTime)<(SELECT outTime FROM tbl_threshold WHERE id = '2')THEN 'Early Out'
                 WHEN t5.Slot ='3' AND max(t1.attnTime)<(SELECT outTime FROM tbl_threshold WHERE id = '3')THEN 'Early Out'
                 WHEN t5.Slot ='4' AND max(t1.attnTime)<(SELECT outTime FROM tbl_threshold WHERE id = '4')THEN 'Early Out'
                 ELSE 'Late-In'
           END) AS Status

    FROM tbl_attn_temp t1, tbl_assigned t3, tbl_batch t5
    JOIN (SELECT DISTINCT attnDate FROM tbl_attn_temp) t2
    WHERE t1.attndate = t2.attnDate and t3.BatchID=t5.BatchID AND t1.TraineeID = t3.TraineeID
    AND t1.attnDate='2016-01-13'
    AND(CASE WHEN t5.Slot ='1' THEN t1.attnTime BETWEEN(SELECT minLimit FROM tbl_threshold WHERE id = '1') AND (SELECT maxLimit FROM tbl_threshold WHERE id = '1') 
             WHEN t5.Slot ='2' THEN t1.attnTime BETWEEN(SELECT minLimit FROM tbl_threshold WHERE id = '2') AND (SELECT maxLimit FROM tbl_threshold WHERE id = '2')
             WHEN t5.Slot ='3' THEN t1.attnTime BETWEEN(SELECT minLimit FROM tbl_threshold WHERE id = '3') AND (SELECT maxLimit FROM tbl_threshold WHERE id = '3')
             WHEN t5.Slot ='4' THEN t1.attnTime BETWEEN(SELECT minLimit FROM tbl_threshold WHERE id = '4') AND (SELECT maxLimit FROM tbl_threshold WHERE id = '4')
        END)
    GROUP BY t1.TraineeID, t2.attnDate
) AS query1

UNION

SELECT * FROM(
SELECT t1.TraineeID,
       t2.attnDate,
       MIN(t1.attnTime) AS inTime,
              (CASE WHEN MIN(t1.attnTime) < MAX(t1.attnTime) THEN MAX(t1.attnTime) else '' end) AS outTime,
       (CASE WHEN t4.Slot ='1' AND t1.attnTime<=(SELECT inTime FROM tbl_threshold WHERE id = '1')THEN 'P' 
             WHEN t4.Slot ='2' AND t1.attnTime<=(SELECT inTime FROM tbl_threshold WHERE id = '2')THEN 'P'
             WHEN t4.Slot ='3' AND t1.attnTime<=(SELECT inTime FROM tbl_threshold WHERE id = '3')THEN 'P'
             WHEN t4.Slot ='4' AND t1.attnTime<=(SELECT inTime FROM tbl_threshold WHERE id = '4')THEN 'P'
             WHEN t4.Slot ='1' AND max(t1.attnTime)<(SELECT outTime FROM tbl_threshold WHERE id = '1')THEN 'Early Out' 
             WHEN t4.Slot ='2' AND max(t1.attnTime)<(SELECT outTime FROM tbl_threshold WHERE id = '2')THEN 'Early Out'
             WHEN t4.Slot ='3' AND max(t1.attnTime)<(SELECT outTime FROM tbl_threshold WHERE id = '3')THEN 'Early Out'
             WHEN t4.Slot ='4' AND max(t1.attnTime)<(SELECT outTime FROM tbl_threshold WHERE id = '4')THEN 'Early Out'
             ELSE 'Late-In'
       END) AS Status


FROM tbl_attn_temp t1, tbl_assigned t3, tbl_instructor_info t4
JOIN (SELECT DISTINCT attnDate FROM tbl_attn_temp) t2
WHERE t1.attndate = t2.attnDate AND t1.TraineeID = t4.InstructorID
AND t1.attnDate='2016-01-13'
AND(CASE WHEN t4.Slot ='1' THEN t1.attnTime BETWEEN(SELECT minLimit FROM tbl_threshold WHERE id = '1') AND (SELECT maxLimit FROM tbl_threshold WHERE id = '1') 
         WHEN t4.Slot ='2' THEN t1.attnTime BETWEEN(SELECT minLimit FROM tbl_threshold WHERE id = '2') AND (SELECT maxLimit FROM tbl_threshold WHERE id = '2')
         WHEN t4.Slot ='3' THEN t1.attnTime BETWEEN(SELECT minLimit FROM tbl_threshold WHERE id = '3') AND (SELECT maxLimit FROM tbl_threshold WHERE id = '3')
         WHEN t4.Slot ='4' THEN t1.attnTime BETWEEN(SELECT minLimit FROM tbl_threshold WHERE id = '4') AND (SELECT maxLimit FROM tbl_threshold WHERE id = '4')
    END)
GROUP BY t1.TraineeID, t2.attnDate
) as query2

попробуйте ключевое слово union all вместо union

пытаться:

select * from (query 1)
union all
(query 2)