Without specifying which, mech automatically selects the first form; you need to select the second form on that url, so:

$mech->submit_form(
    form_number => 2,
    fields =>{
        sess => "summer",
        course => $prefix,
        },
    );
[download]

gives me something.

UPDATE:...and that something wasn't good.

I've always found it easier to debug form automation in WWW::Mechanize by doing one thing at a time. This works for me:

use WWW::Mechanize;
use HTML::TokeParser;
my $mech = WWW::Mechanize->new(cookie_jar => undef);
$url="http://www.utsc.utoronto.ca/~registrar/scheduling/timetable";
$prefix = "ANT";
$mech->get($url);

$mech->form_number(2);
$mech->set_visible( [radio => 'summer'] );  # page default anyway
$mech->select( 'course', $prefix );
$mech->click_button( name => 'submit' );

print $mech->content();
[download]

- clarified first sentence.