(the properties for this issue aren't optimal, but it is not possible to e.g. tag it with Component = code and documentation)
the typo3 site is still active, so maybe some users are deleted there but are still on the drupal site, because the where imported in one other migration.

Or your migrate_maps_* tables are not valid and you want to be certain all imported users are the only users on the drupal site (ok guest and admin, with uid = 0 and 1 are keept anyway) .

if you want to use this add this code into the class Typo3FeUserMigration, and execute the Typo3BeUser - migration first

  /**
   * Remove users that were deleted in the source.
   */
  public function postImport() {
    // delete users, that are not in the actual source, the source are
    // two tables: the backend- and frontend-users
    // the destination is the {users}-table of drupal
    $uids = db_select('users', 'u')
              ->fields('u', array('uid', 'name'))
              ->condition('uid', 1, '>') // no guest and no admin
              ->execute()
              ->fetchAllKeyed(); // fetch all users into $uids[uid]='name'

    $beusers = db_select(TYPO3_DATABASE_NAME . '.be_users', 'u')
                ->fields('u', array('username', 'uid', 'disable'))
                ->condition('u.deleted', '0')
                ->condition('u.disable', $this->queryParams['beuser']['disable'], $this->queryParams['beuser']['disable_operator'])
                ->execute()
                ->fetchCol(); // build an array $beusers[xx]='username'

    $feusers = db_select(TYPO3_DATABASE_NAME . '.fe_users', 'u')
              ->fields('u', array('username', 'uid', 'disable'))
              ->condition('u.deleted', '0')
              ->condition('u.disable', $this->queryParams['feuser']['disable'], $this->queryParams['feuser']['disable_operator'])
              ->execute()
              ->fetchCol(); // build an array $beusers[xx]='username'

    // array $uids without $beusers and $feusers -> delete these uids
    $delete = array_diff($uids, $beusers, $feusers);
    user_delete_multiple(array_keys($delete)); // in the key is the uid for durpal
  }