It looks to me that this is not doing what you think:

my %count = ();
foreach my $device (@current_list, @temp_devicelist) {
    $count{$device}++;
}
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as those arrays are in fact arrays of arrays. Try getting rid of that and putting my %count at the top of your sub and counting within the other loops:

my %count;
# ...
for ($n=0; $n < $size; $n++) {
    our $device=$current_list[$n][0];
    $count{$device}++;
}
# ...
for ($n=0; $n < $size; $n++) {
    our $tempdevicelinks=$temp_list[$n][0];
    $count{$tempdevicelinks}++;
}
# ...
my @difference = grep { $count{$_} == 1 } keys %count;
my @intersect  = grep { $count{$_} == 2 } keys %count;
my @union      = keys %count;
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Then you can print out the values:

print "Difference:\n";
print "$_\n" for @difference;
print "Intersect:\n";
print "$_\n" for @intersect;
print "Union:\n";
print "$_\n" for @union;
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