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I generated an sitemap.xml file through the Catalog > Google sitemap area.

What I experience is that the product url's in the .xml appears to be incorrect url-path'wise.

So a product url appears as: http://www.domain.com/product1.html

While the correct on-site canonical url would be: http://www.domain.com/category1/subcat/product1.html

In Configuration > Catalog > SEO, all is set to Yes/activated.

Any ideas on why this is happening and how it can be fixed?

1

This is not a bug, It's a feature.
take a look at how the products are retrieved for generating the xml sitemap.
Mage_Sitemap_Model_Resource_Catalog_Product::getCollection()

    $urCondions = array(
        'e.entity_id=ur.product_id',
        'ur.category_id IS NULL',
        $this->_getWriteAdapter()->quoteInto('ur.store_id=?', $store->getId()),
        $this->_getWriteAdapter()->quoteInto('ur.is_system=?', 1),
    );

The code above represents the join condition with the url rewrites table.
So the url retrieved is the one that has the category_id set to NULL.
This translates into www.somewebsite.com/product-url.html.

If you want to change this functionality, you can try to rewrite this piece of code to include a url rewrite where the category_id is not NULL. but this may lead to strange results, because the products can be places in 0 to all categories.

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