Also, check the return values of your ftp commands. There may be a failure and FTP will not clean up after itself.

#!/usr/bin/perl -wd

use strict;
use warnings;
use Net::FTP;

my $file  = "ftp.pl";
my $host = "some_host";
my $user = "a_user";
my $pass = "the_pass";
my $ftp  = Net::FTP->new( $host ) or die "Could not open $host\n";

$ftp->login( $user, $pass ) or die "Could not login\n";
$ftp->put( $file ) or die "Could not put $file\n";
$ftp->quit();
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-derby

update: Updated the error messages (thanks runrig and see Beginners guide to Net::FTP).