I have resolved this use case by adding TRACK HISTORY ON to the APPLY CHANGES INTO and removed the DISTINCT keyword. 

APPLY CHANGES INTO LIVE.targettable
FROM ( SELECT * 
FROM STREAM(sourcetable_1) tbl1
INNER JOIN STREAM(sourcetable_2) tbl2 ON tbl1.id = tbl2.id
WITH WATERMARK AS (tbl1.createddate))
KEYS (col1, col2) IGNORE NULL UPDATES SEQUENCE BY (createddate) STORED AS SCD TYPE 2
TRACK HISTORY ON * EXCEPT (col1,col2);

 Hope this helps to someone.

Thanks.