People may still be able to see if you're friends with someone, even if you've selected "Only me" in the privacy settings. This scenario occurs because they can see the "Friends' list of others who are also friends with you unless that user also restricted them. If they can see that you're friends with someone via their profile, they can also access this information from the 'News Feed,' as well as 'Search,' and many other options on Facebook. Yes, this includes the 'Mutual friends' view.