Test case:

    CREATE TABLE t (label VARCHAR(10), step INTEGER);
    INSERT INTO T VALUES('a', 1);
    INSERT INTO T VALUES('a', 1);
    INSERT INTO T VALUES('b', 1);
    WITH RECURSIVE cte(label, step) AS (
        SELECT DISTINCT * FROM t 
      UNION ALL 
        SELECT label, step + 1 FROM cte WHERE step < 3
    )
    SELECT * FROM cte;

The above should return 6 rows, but is returning 9 rows with all recent versions of SQLite. That 6 rows are correct is confirmed on sqlfiddle.com using PostgreSQL and SQL Server.

Bisect shows the problem first appeared in check-in 45d8cc678d128f1d on 2014-03-21 (6.5 years ago!) and was first released with version 3.8.5. The problem has not been reported from the field in all that time, which tells us that it is not a high priority to fix.

Problem reported on the Forum via post 1d3b0519e2.