I could only think you need to add error handling in your code

Example: you can think of following code to handle the duplicate key issue

BEGIN TRY

CREATE UNIQUE CLUSTERED INDEX ix_tblname ON tblname (col1,col2)

END TRY

BEGIN CATCH

;WITH dupes AS

(SELECT * , ROW_NUMBER() OVER ( PARTITION BY col1,col2 ORDER BY col1, col2) AS Rownum FROM tblname )

DELETE FROM dupes

OUTPUT DELETED.* INTO #Log

WHERE Rownum > 1

CREATE UNIQUE CLUSTERED INDEX ix_tblname ON tblname (col1,col2)

END CATCH