This is a known bug in Magento: Magento categories are not displaying the correct amount of products even when you reindex the website. To fix this you need to be experienced in using phpmyadmin. Issue the following command and then wait for a response (it can take a few minutes)

DELETE FROM  catalog_category_product  where product_id NOT IN (SELECT entity_id FROM (catalog_product_entity))

Now reindex via the Magento admin and then check your categories. The product count in the Magento categories are now showing correct numbers.