Since API v2.0, you (after granting user_friends
permission) can only get the list of mutual friends with a user that also granted user_friends
permission. The list will only have mutual friends that are using your app and granted user_friends
permissions.
Please, see https://developers.facebook.com/docs/graph-api/reference/v2.0/user.context/mutual_friends
Cheers!
Update: The All Mutual Friends API feature was deprecated for Graph API v3.1 on July 26, 2018, and will be deprecated for all versions on October 24, 2018.
https://developers.facebook.com/docs/apps/review/feature#reference-ALL_MUTUAL_FRIENDS