Why are two url aliases being generated for some users? I have a site under development, that is a migration from an different cms via the Migrate module. I noticed that the links for a lot of my user profiles are not staff/lastname-firstname as I set in the pathauto settings, but /firstname-lastname.

Looking in the url_alias table I see one alias for staff/lastname-firstname (pid 1644030) and another one (pid 1644031) for firstname-lastname. I point out the pids just because it appears that they are probably being created one after the other. They are both marked as language undefined, most likely due to the neutral path module. I suspect that one of the aliases was originally meant to be for English and the second for Japanese, but there is no setting in pathauto for different language paths for users. I can try disabling the neutral path module and rerunning my migration to confirm that they were each meant for different languages, but how can I fix it? I do not need a /firstname-lastname path in the system. I only want /staff/lastname-firstname to be generated.
Then first go to /admin/config/search/path/delete_bulk and delete the aliases in question.

Disable Pathauto for the migration process. 

Once your site has been migrated, then enable pathauto and do a bulk update /admin/config/search/path/update_bulk