Here's the basics of a CTE-based approach :
With Merged AS
( -- CTE 1 : All Data in one table
SELECT * FROM table1
UNION ALL
SELECT * FROM table2
UNION ALL
SELECT * FROM table3
)
, Multiples AS
( -- CTE 2 : Group by the fields in common
SELECT Col1, Col2
FROM Merged
GROUP BY Col1, Col2
HAVING Count(*)>1 -- only want Groups of 2 or more
)
SELECT
Merged.*
FROM Merged INNER JOIN Multiples
-- Only return rows from Merged if they're in Multiples
ON Merged.[Col1]=Multiples.[Col1]
AND Merged.[Col2]=Multiples.[Col2]
Something like that works with my own example MS-SQL data, and it looks like SQLite syntax is the same. HTH!