I'm using the UserGroup.GetAllUserCollectionFromWeb method to return all the users in a Site Collection: https://msdn.microsoft.com/en-us/library/websvcusergroup.usergroup.getallusercollectionfromweb(v=office.14).aspx
When used, the result set includes users that are no longer in the site and or can't be validated through the Check Permissions modal. (Site Actions --> Site Permissions --> Check Permissions).
Result set:
userA (valid)
userB (can't validate in modal)
userC (valid)
userD (valid)