SQL Server 2016

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declare @t table (NIP  varchar(100), [NAME] varchar(100), DEPARTMENT varchar(100), STATUSIN datetime, STATUSOUT datetime, LATECOME TIME)
insert into @t select 'A1', 'ARIA',  'BB', '2020-01-21 08:06:23', '2020-01-21 11:58:36', '00:06:23'             
insert into @t select 'A1', 'ARIA',  'BB', '2020-01-22 07:34:27', '2020-01-22 17:19:47', '00:00:00'               
insert into @t select 'A1', 'ARIA',  'BB', '2020-01-23 08:30:00', '2020-01-23 11:00:00', '00:30:00'
insert into @t select 'A1', 'ARIA',  'BB', '2020-01-24 08:05:00', '2020-01-24 10:30:00', '00:05:00'
insert into @t select 'A2', 'BELLE', 'BB', '2020-01-21 07:06:20', '2020-01-21 13:58:31', '00:00:00'             
insert into @t select 'A2', 'BELLE', 'BB', '2020-01-22 07:34:27', '2020-01-22 17:19:47', '00:00:00'               
insert into @t select 'A2', 'BELLE', 'BB', '2020-01-23 07:06:00', '2020-01-23 10:30:00', '00:00:00'
insert into @t select 'A2', 'BELLE', 'BB', '2020-01-24 09:06:00', '2020-01-23 10:30:00', '02:06:00'
insert into @t select 'A3', 'CHLOE', 'CC', '2020-01-21 07:06:23', '2020-01-21 11:55:30', '00:00:00'             
insert into @t select 'A3', 'CHLOE', 'CC', '2020-01-22 07:34:27', '2020-01-22 17:00:44', '00:00:00'               
insert into @t select 'A3', 'CHLOE', 'CC', '2020-01-23 08:37:00', '2020-01-23 11:13:00', '00:37:00'
insert into @t select 'A3', 'CHLOE', 'CC', '2020-01-24 08:09:00', '2020-01-24 10:22:00', '00:09:00'
insert into @t select 'A4', 'ZIYA',  'CC', '2020-01-21 07:06:20', '2020-01-21 13:58:31', '00:00:00'             
insert into @t select 'A4', 'ZIYA',  'CC', '2020-01-22 07:34:27', '2020-01-22 17:19:47', '00:00:00'               
insert into @t select 'A4', 'ZIYA',  'CC', '2020-01-23 06:06:00', '2020-01-23 11:30:00', '00:00:00'
insert into @t select 'A4', 'ZIYA',  'CC', '2020-01-24 09:06:00', '2020-01-23 15:30:00', '02:06:00'
insert into @t select 'A1', 'BRIAN',  'BB', '2020-01-21 08:06:23', '2020-01-21 11:58:36', '00:06:23'             
insert into @t select 'A1', 'BRIAN',  'BB', '2020-01-22 07:34:27', '2020-01-22 17:19:47', '00:00:00'               
insert into @t select 'A1', 'BRIAN',  'BB', '2020-01-23 08:30:00', '2020-01-23 11:00:00', '00:30:00'
insert into @t select 'A1', 'BRIAN',  'BB', '2020-01-24 08:05:00', '2020-01-24 10:30:00', '00:05:00'

SELECT * FROM @t;
;WITH cte AS 
(
	SELECT DISTINCT [NAME], DEPARTMENT, MONTH(STATUSIN) [MONTH], YEAR(STATUSIN) [YEAR], 
        SUM(CASE WHEN LATECOME = '00:00:00' THEN 0 ELSE 1 END) OVER(PARTITION BY [NAME], DEPARTMENT, MONTH(STATUSIN), YEAR(STATUSIN) ORDER BY [NAME]) Total
    FROM @t
)

select DEPARTMENT, [MONTH], [YEAR], SUM(CASE WHEN TOTAL > 2 THEN 1 ELSE 0 END) LATECOME
from cte
GROUP BY DEPARTMENT, [MONTH], [YEAR]

NIP	NAME	DEPARTMENT	STATUSIN	STATUSOUT	LATECOME
A1	ARIA	BB	2020-01-21 08:06:23.000	2020-01-21 11:58:36.000	00:06:23
A1	ARIA	BB	2020-01-22 07:34:27.000	2020-01-22 17:19:47.000	00:00:00
A1	ARIA	BB	2020-01-23 08:30:00.000	2020-01-23 11:00:00.000	00:30:00
A1	ARIA	BB	2020-01-24 08:05:00.000	2020-01-24 10:30:00.000	00:05:00
A2	BELLE	BB	2020-01-21 07:06:20.000	2020-01-21 13:58:31.000	00:00:00
A2	BELLE	BB	2020-01-22 07:34:27.000	2020-01-22 17:19:47.000	00:00:00
A2	BELLE	BB	2020-01-23 07:06:00.000	2020-01-23 10:30:00.000	00:00:00
A2	BELLE	BB	2020-01-24 09:06:00.000	2020-01-23 10:30:00.000	02:06:00
A3	CHLOE	CC	2020-01-21 07:06:23.000	2020-01-21 11:55:30.000	00:00:00
A3	CHLOE	CC	2020-01-22 07:34:27.000	2020-01-22 17:00:44.000	00:00:00
A3	CHLOE	CC	2020-01-23 08:37:00.000	2020-01-23 11:13:00.000	00:37:00
A3	CHLOE	CC	2020-01-24 08:09:00.000	2020-01-24 10:22:00.000	00:09:00
A4	ZIYA	CC	2020-01-21 07:06:20.000	2020-01-21 13:58:31.000	00:00:00
A4	ZIYA	CC	2020-01-22 07:34:27.000	2020-01-22 17:19:47.000	00:00:00
A4	ZIYA	CC	2020-01-23 06:06:00.000	2020-01-23 11:30:00.000	00:00:00
A4	ZIYA	CC	2020-01-24 09:06:00.000	2020-01-23 15:30:00.000	02:06:00
A1	BRIAN	BB	2020-01-21 08:06:23.000	2020-01-21 11:58:36.000	00:06:23
A1	BRIAN	BB	2020-01-22 07:34:27.000	2020-01-22 17:19:47.000	00:00:00
A1	BRIAN	BB	2020-01-23 08:30:00.000	2020-01-23 11:00:00.000	00:30:00
A1	BRIAN	BB	2020-01-24 08:05:00.000	2020-01-24 10:30:00.000	00:05:00

DEPARTMENT	MONTH	YEAR	LATECOME
BB	1	2020	2
CC	1	2020	0