After updating Net::FTPSSL and the modules that go with it i was able to force the connection i needed.
While it's suggested to not do this. It appears to be necessary in my case.

use Net::FTPSSL;

my $ftps = Net::FTPSSL->new(
    'site.uat.mysite.com',
    Encryption             => EXP_CRYPT,
    Debug                  => 1,
    DebugLogFile           => "myLog.txt",
    Port                   => 5041,
    useSSL                 => 0,
    SSL_Client_Certificate => {
        SSL_cert_file => '/path/to/cert_file.pem',
        SSL_passwd_cb => sub { return 'pa$$w0rd' },
        SSL_version   => 'TLSv12',
    },
    Croak => 1
);

$ftps->trapWarn();    # Only call if opening a CPAN bug report.

$ftps->login( 'USERNAME', 'PASSWORD' );


$ftps->put( "test.txt", "test1.txt" );
foreach ( $ftps->list() ) {
    print "$_\n";
}

$ftps->get("test1.txt");

$ftps->quit();
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