If we go with the assumption that an element never occurs more than once in a single array, we don't need to track the arrays seperately, and can use Perl's array flattening:

my %present;
for my $a ( @array1, @array2, @array3 ) { $present{ $a }++ }
my @only_two = grep $present{ $_ } == 2, keys %present;
[download]

If we have to deal with multiples in any of the arrays:

use List::MoreUtils qw(uniq);
my %present = ();
for my $a ( uniq(@array1), uniq(@array2), uniq(@array3) ) { $present{ 
+$a }++ }
my @only_two = grep $present{ $_ } == 2, keys %present;
[download]