my $Hash = {
    "A" => ["HYU"],
    "B" => ["TU6"],
    "C" => [ "11", "09", "88", "2" ],
    "D" => [ "01", "11" ]
};

##</code><code>##

A,	B,	C,	D
HYU	TU6	11	01	
		      09	11	
		      88		
		      2		
 
##</code><code>##

use warnings;
use strict;

my $Hash = {
    "A" => ["HYU"],
    "B" => ["TU6"],
    "C" => [ "11", "09", "88", "2" ],
    "D" => [ "01", "11" ]
};

# get headiing
print join( ",\t" => sort keys %$Hash ), $/;

# get the value with the highest numbers of element
my $highest_item = 0;

foreach ( keys %{$Hash} ) {
    my $value = scalar @{ $Hash->{$_} };
    $highest_item = $value if $highest_item < $value;
}

# re-write the data given as AoA, with data needed
my @final_data;

foreach my $key ( sort keys %{$Hash} ) {

    push @final_data =>
      [ map { $Hash->{$key}[$_] || qq[] } 0 .. ( $highest_item - 1 ) ];
}

# print out in expected output
foreach my $pos ( 0 .. $#final_data ) {
    foreach ( 0 .. $highest_item - 1 ) {
        print $final_data[$_][$pos], "\t";
    }
    print $/;
}