Wrong results from joining two CTEs
As the discussion in the comments revealed, an fcontainer can be related to many products, due to the 1-to-many relationship between FContainer and Stämplingar.

Try this query, which will choose only one product per fcontainer.

The missing fcontainers are due to the INNER join. Changing it to LEFT join will show all fcontainers, even those not related to any product:

;WITH CTE1 AS
(
    SELECT 
        FContainerHylla.Name, FContainerPlats.HyllId,
        FContainerPlats.x, FContainerPlats.y,
        FContainerPlats.enable, FContainerHylla.Type,
        ISNULL( (SELECT MIN(fcontainer.id) AS id
                 FROM FContainer
                 WHERE (PlatsId = FContainerPlats.id)
                ), 0) AS FcId 
    FROM FContainerPlats 
      INNER JOIN FContainerHylla ON FContainerPlats.HyllId = FContainerHylla.Id
    WHERE (FContainerHylla.Type IN (1, 6, 10))
),

    CTE2 AS 
(
    SELECT 
        FContainer.id AS SubID, MIN(produkter.Produktnamn) AS Produktnamn
    FROM FContainer 
      INNER JOIN Stämplingar ON FContainer.id = Stämplingar.ID 
      INNER JOIN Tempo ON Stämplingar.temponr = Tempo.temponr 
      INNER JOIN Produkter ON Tempo.produktnr = Produkter.Produktnr
    GROUP BY 
         FContainer.id
) 

SELECT CTE1.*, CTE2.Produktnamn
FROM CTE1
  LEFT JOIN CTE2 ON CTE2.SubID = CTE1.FcId
ORDER BY CTE1.HyllId, CTE1.x, CTE1.y ;