#!/usr/bin/perl
use strict;
use warnings;
use Data::Dumper;
use Array::Utils qw(:all);

my %HoA1 = (
    Fruits    => [ "Apple", "Orange", "Banana", "Grapes" ],
    Fruits1   => [ "WaterMellon" ],
    );

my %HoA2 = (
    Fruits    => [ "Apples", "Orange", "pineapple", "Grapes" ],
    Fruits1   => [ "Mellon" ],
    );

my @AoAValues1 = sort values %HoA1;
my @AoAValues2 = sort values %HoA2;

my %hash;
for (0 .. $#AoAValues1) {
    $hash{$_} = [ array_minus( @{$AoAValues2[$_]}, @{$AoAValues1[$_]} ) ];
}

print Dumper \%hash;

__END__

$ perl test.pl
$VAR1 = {
          '0' => [
                   'Apples',
                   'pineapple'
                 ],
          '1' => [
                   'Mellon'