Better done using a single hash (didn't test this, use at your own risk. Should work, though):

use strict;
use warnings;

my %in_files;

open(my $f1, '<', 'FILE1') or die "can't open FILE1: $!\n";
while (<$f1>) {
    $in_files{$_} .= '1';
}

open(my $f2, '<', 'FILE2') or die "can't open FILE2: $!\n";
while (<$f2>) {
    $in_files{$_} .= '2';
}

open(my $common, '>', 'common_lines') or die "can't open common_lines:
+ $!\n";
open(my $u1, '>', 'unique_1') or die "can't open unique_1: $!\n";
open(my $u2, '>', 'unique_2') or die "can't open unique_2: $!\n";
for (keys %in_files) {
    if ($in_files{$_} =~ m/12/) { print $common $_ }
    else if ($in_files{$_} =~ m/1/) { print $u1 $_ }
    else { print $u2 $_ }
}
[download]