A bit more perlish. Note that %a is not really necessary. And the keys could be pre-sorted.

#!/usr/bin/perl
use strict;

my @a  = qw( AA BB CC DD EE FF );
my @a1 = qw( AA DD EE );
my @a2 = qw( AA BB CC FF );

my %a  = map { $_ => 1 } @a;
my %a1 = map { $_ => 1 } @a1;
my %a2 = map { $_ => 1 } @a2;

my (@tmp1, @tmp2);

@tmp1 = map { exists $a1{$_} ? $_ : '##' } sort keys %a;
@tmp2 = map { exists $a2{$_} ? $_ : '##' } sort keys %a;

print join(',',@tmp1);
print "\n";
print join(',',@tmp2);
print "\n";
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update: removed unnecessary parentheses