The URL rewrites of Magento 2 will not be reindexed when rebuilding the index via command line. I recommend using https://github.com/olegkoval/magento2-regenerate_url_rewrites to include the reindex of URL rewrites on the shell. This Magento 2 extensions allows for reindexing all URL rewrites.
After installation, run these 2 commands:
php bin/magento cache:flush
php bin/magento cache:clean
Now just reindex as usual, the rewrites will be included.