hreflang links added to page source without translation
These are added via a hook_page_attachments() implementation in content_translations.module. The code looks like it should not add any hrefs unless an entity translation has been created. 

Some tests on my site seem to indicate that this is working correctly.  Do you have another module that is trying to add these and doing it incorrectly?

That said, you should be able to implement a hook_page_attachments() function (in something with a execution weight that runs after the content code).  In this look at the $page['#attached']['html_head_link'] array for the items to remove.