Вероятно искате да използвате GROUP BY клауза вместо с DISTINCT там, т.е.:
SELECT productId, Size,
SUM(CASE WHEN storeID IN ('BCN', 'BCN2') THEN stock ELSE 0 END) AS stockBCN,
SUM(CASE WHEN storeID = 'MAD' THEN stock ELSE 0 END) AS stockMAD
FROM stocks
GROUP BY productId, Size
