I'm think you need to change your code something like that:

my @hashes;

foreach my $filename (@filenames) {
  open my $fh, "<", $filename or die "Can't open $filename: $!";
  binmode $fh;
  push @hashes, [ Digest::MD5->new->addfile($fh)->hexdigest, $filename
+ ];
  close $fh;
}
my @sorted = sort { $a->[0] cmp $b->[0] } @hashes;
print "$sorted[0]  $sorted[1]\n";
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Update: Fixed error with array vs. arrayref (thanks to oshalla).