Two tables, same Attributes unable to count,
You could try to fetch all affected records of both tables using UNION ALL and then COUNT the records. (I'm not sure if you want to COUNT records or to SUM quantities.)

Notice you should add transaction_type to the GROUP BY clause.

If you want you can move the WHERE clause to the main query.

SELECT transaction_type, sku, COUNT(quantity_purchased) as SKU_ORDER
FROM   (
        SELECT transaction_type, sku, quantity_purchased
        FROM   settlements_qty_test
        WHERE  transaction_type = 'order'
        AND    amount_description = 'Principal'
        AND    amount_type = 'ItemPrice'   
        UNION ALL
        SELECT transaction_type, sku, quantity_purchased
        FROM   settlements_qty_test1
        WHERE  transaction_type = 'order'
        AND    amount_description = 'Principal'
        AND    amount_type = 'ItemPrice'   
       ) t1
GROUP BY transaction_type, sku
ORDER BY sku;