Is gobbling an entire file into an array considered bad form? . . .

One should always be aware of the efficiency concern. If you're sure the file will never be "too big", sluurping (as it's called) shouldn't be a problem. Otherwise, you'd do well to try to do per-record reading/processing, where practical.

Calin's solution is good. If you want a little extra efficiency, you can buy it with memory, i.e. data structures. In the solution below, we maintain a separate hash for those keys which are known to be duplicates. Then, at the end, we iterate only over that hash. This has a pay-off if the number of duplicate keys is significantly smaller than the total number of keys.

my( %keys, %dup );
while (<STDIN>)
{
   chomp;
   if ( /PROBABLECAUSE\w*\((\d+),\s*\w*,\s+(\w*)/ )
   {
      my( $id, $key ) = ( $1, $2 );
      if ( exists $dup{$key} ) # already found to be a dup
      {
         push @{ $dup{$key} }, $id;
      }
      elsif ( exists $keys{$key} ) # only seen once before
      {
         push @{ $dup{$key} }, delete($keys{$key}), $id;
      }
      else # first time seen
      {
         $keys{$key} = $id;
      }

      # check if any key has init caps (not allowed)
      if ( $key =~ /^[A-Z]\w*/ )
      {
         print "Id: $id - $key\n";
      }
   }
}

print "\nDuplicated keys:\n\n";
for my $key ( keys %dup )
{
   print "Key: $key\n";
   print "\tId: $_\n" for @{$dup{$key}};
}
[download]