return duplicate value from duplicate data in where clause in sql

Based on the description the two rows containing

kti001
kti001

are not duplicates. Otherwise the SELECT statement would return both of those.

In SQL if you want to eliminate duplicate rows you need to specify DISTINCT in your query. Since you haven't used that keyword, duplicates are allowed.

Having that said the only option is that there is a difference between the rows, perhaps a trailing space or something.

To find out the differences have a try with something like this on your dynamic data

select '>' + empid  + '<' from table

That should help you to visualize possible spaces within the data.

[Edit]
As an example that using an IN operator does not remove duplicates, consider the following statements:
Create the test table

CREATE TABLE TestTable1 (
   EmpId   VARCHAR(MAX)
);

Add initial rows

INSERT INTO TestTable1 (EmpId) VALUES ('kti001');
INSERT INTO TestTable1 (EmpId) VALUES ('kti001');
INSERT INTO TestTable1 (EmpId) VALUES ('kti002');

Select without DISTINCT

SELECT EmpId FROM TestTable1 WHERE EmpID in ('kti001','kti001','kti002')

Result

EmpId
------
kti001
kti001
kti002

Select with DISTINCT

SELECT DISTINCT EmpId FROM TestTable1 WHERE EmpID in ('kti001','kti001','kti002')

Result

EmpId
------
kti001    <-- duplicate removed
kti002

Add a non duplicate row with extra space in the beginning

INSERT INTO TestTable1 (EmpId) VALUES (' kti001');

Select

SELECT EmpId FROM TestTable1 WHERE EmpID in ('kti001','kti001','kti002')

Results, the newly added row isn't listed since it does not satisfy the condition

EmpId
------
kti001
kti001
kti002

List the content of the table

SELECT '>' + EmpId + '<' FROM TestTable1 

Result

(No column name)
----------------
>kti001<
>kti001<
>kti002<
> kti001<

Its impossible to say if an extra space is the problem or something else but the main point is that duplicates aren't removed from the result set without DISTINCT keyword.