Yes. Currently the max friends that you can have and work effectively with our service is 5000. We probably will fix this in the future.
Most likely this friend disabled their account from 3rd party app access, blocked UnfriendedYou.com from accessing their info, or they disabled their account then turned it back on which people seem to do all the time. When this happens it prevents external applications like ours from being able to see them on the facebook network.
We can't see why you're not friends with someone. We can only detect when someone ceases being your friend. So when you unfriend or unfollow someone its going to see that as the same thing as them unfriending you.