use strict;
use Data::Dumper;

my %hash = qw/ A 1 B 2 /;

print 'Before sub:'.Dumper(\%hash);
modify_hash(\%hash);
print 'After sub:'.Dumper(\%hash);

sub modify_hash{
 my $h_ref = shift;

 $h_ref->{C}    = '3';
 $h_ref->{D}    = '4';
 %{$h_ref}->{E} = '5';  # this is what it's doing
 $$h_ref{F}     = '6';  # you could do this too
}

##</code><code>##

Before sub:$VAR1 = {
          'A' => '1',
          'B' => '2'
        };
After sub:$VAR1 = {
          'F' => '6',
          'A' => '1',
          'B' => '2',
          'C' => '3',
          'D' => '4',
          'E' => '5'
        };