Assuming that there are no two equal lines in one file and files are not too big two simple loops will do the job:

#!/usr/bin/perl

$fnx = "file1";
$fny = "file2";
$fnz = "file.uncommon";
$fntmp = "file.common";
open FPX, "$fnx" or die "Error in write:$!";
open FPY, "$fny" or die "Error in write:$!";
open FPZ, ">$fnz" or die "Error in write:$!";
open FPTMP, ">$fntmp" or die "Error in write:$!";
@x_lines = map {s/^\s+//; s/\s+$//; $_ } <FPX>;
@y_lines = map {s/^\s+//; s/\s+$//; $_ } <FPY>;

for $xnr(1..@x_lines)
{
    $x = $x_lines[$xnr-1];
    $matched = 0;
    for $ynr(1..@y_lines)
    {
        $y = $y_lines[$ynr-1];
        if($x eq $y)
        {
            print "Saving matched at $xnr\n";
            print FPTMP "$x \n";
            $matched = 1;
            last;
        }
    }
    if(!$matched)
    {
        print "Saving unmatched at $xnr\n";
        print FPZ "$x \n";
    }
}
close FPX;
close FPY;
close FPZ;
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