A better way to do it is collect what you need first, then do the comparison, that is:

• Make a hash
• For each element in each list, add the list # to the hash for that element if not already on there
• For each key of the hash, if the list has more than 1 item, it's duplicated.

Programmically, it would look like:

my %hash;
foreach my $i ( 0..$#array ) {
   foreach my $j ( @{ $array[ $i ] } ) {
      $hash{ $j } ||= [];  #need to set this if not made
      if ( ! grep { $i == $_ } @{ $hash{ $j } } ) {
         push @{ $hash{ $j } }, $i;
      }
   }
}
my @matches = grep { @{ $hash{ $_ } } > 1 } keys %hash;
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This is probably close to being on the order of N^2 (N being the total number of elements in the entire 2d structure), but will be closer to N as the number of possible duplicates drop.

Note that if you wish to exclude elements, you can simply add an "if (something) next" line in the deepest block, or do an additional grep on the @{ $array } in the second foreach block to remove elements you don't care about. But it's probably faster to look at everything, then drop what you don't need then checking every time.

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Dr. Michael K. Neylon - mneylon-pm@masemware.com || "You've left the lens cap of your mind on again, Pinky" - The Brain