Hi,
Aliases are used to 301 redirect one SEF URL to another. For more detailed information please see JoomSEF's documentation:
www.artio.net/joomsef/documentation#aliases
If there are different non-SEF URLs, you can't prevent them from reappearing. But if both URLs display the same page, it's OK that they have the same SEF URL generated - otherwise they would be seen as a duplicate content.
So I'd suggest just to leave the duplicate as it is if your website is working correctly with it. Google will see only one en/faq URL for the same pages and that's correct.
Such duplicates appear when a component uses different URLs for the same page, which ideally shouldn't happen, but many Joomla components do this.