What did you expect it to print?

use Data::Dumper;

my %hash = (
      'hi' => ('hello' => 'all'),
      'bye' => ('later' => 'gone')
      );

print Dumper \%hash;
__END__
$VAR1 = {
          'hi' => 'hello',
          'later' => 'gone',
          'all' => 'bye'
        };
[download]

The "sublists" that you think you have get flattened into one list qw( hi hello all bye later gone ).

Perhaps you want:

my %hash = (
      'hi' => {'hello' => 'all'},
      'bye' => {'later' => 'gone'}
      );
[download]

See perlreftut and perlref.