I think you basically want to compare two arrays which you get by de-referencing values for each key:

#!/usr/bin/perl
use strict;
use warnings;

my %hash1 = ( abc => [ 1, 2, 3, 4 ], cde => [ 4, 5, 6 ] );
my %hash2 = ( abc => [ 1, 3 ], cde => [ 4, 5 ] );

my @hash1only;

for my $key ( keys %hash1 ) {
    my @array1 = @{ $hash1{$key} };
    my @array2 = @{ $hash2{$key} };

    # build lookup table
    my %seen;
    foreach my $element (@array2) { $seen{$element} = 1 }

    # find only elements in @array1 and not in @array2
    foreach my $element (@array1) {
        unless ( $seen{$element} ) {
            push @hash1only, $element;
        }
    }
}

@hash1only = sort @hash1only;
print "Elements in \%hash1 and not in \%hash2: @hash1only\n";
[download]