So which one is it— Longest common subsequence problem or Longest common substring problem? You speak of subsequences, but the chosen tool is looking for substrings.

If the intention was to look for the longest common substring, then you could essentially

  my $s1 = join $stop_character1, @array1;
  my $s2 = join $stop_character2, @array2;
  lcss($s1, $s2);
[download]

... and be done with that.