Here is the loop that is reading from the file, as requested. The whole script is a couple hundred lines, I can post it if you think it's necessary, but I think the problem is here. I'm using strict and warnings, just so you know.

my $HTML = $query->param(-name=>"file");

print $query->header;
print $query->start_html("Class Schedule");

while (<$HTML>) {
#    if (/SEE SCHEDULE OF CLASSES/) {
#       next;
#    }
    if (/^<(?:TR).*?>(\d{5}).*?>(\d{2}).*?>(\d{3}).*?>(\d{3}).*?>(\d{2
+}).*?>(?:[&\w]).*?>(\w+(?:(?:[\s\w|&]+)?)*).*?>\s(\d).*?>(\w*?\d(?:[,
+\d\*]?)*)((?:[\w\d,]?)+).*?>(\w(?:(?:[\w\d-])?)*).*?<\/TR>(<.*)?/i) {
        push(@classid, $1);
        my $rec = join("", split(/,/, $9));
        my $h_fix = join("", split(/,/, $8));
        $rec =~ tr/H/h/;
        $h_fix =~ tr/H/h/;
        push(@classes, $h_fix);
        push(@class, parse($h_fix));
        push(@location, $10);
        my @mi2 = ($2, $3, $4, $5);
        push(my @misc_info, \@mi2);
        push(@credits, $7);
        my $short_name = $6;
        $short_name =~ s/&/ AND /;
        push(@classname, $short_name);
        if ($h_fix =~ /\*$/) {
            push (@starperiod, "*");
        }
        else {
            push(@starperiod, "");
        }
        if ($9) {
            push(@classes, $rec);
            push(@class, parse($rec));
            push(@classid, $1);
            push(@location, $10);
            push(@misc_info, \@mi2);
            push(@credits, $7);
            push(@classname, $short_name);
            if ($rec =~ /\*$/) {
               push (@starperiod, "*");
            }
            else {
                push(@starperiod, "");
            }
        }
        my @erec;
        if ($11) {
            my @temprec;
            @erec = $11 =~ />(.*?)</g;
            for (my $z = 0; $z < @erec; $z++) {
                my $rectemp;
                if ($erec[$z] =~ /^&/) {
                }
                else {
                    if ($erec[$z] =~ /\*$/) {
                        push (@starperiod, "*");
                        chop($erec[$z]);
                        $rectemp = $erec[$z];
                    }
                    else {
                        $rectemp = $erec[$z];
                    }
                    push(@temprec, $rectemp);
                }
            }
            my $temprec_fix = $temprec[10];
            $temprec_fix =~ tr/H/h/;
            push(@classid, $classid[-1]);
            push(@classes, $temprec_fix);
            push(@class, parse($temprec_fix));
            push(@location, $temprec[14]);
            push(@misc_info, \@mi2);
            push(@credits, $credits[-1]);
            push(@classname, $short_name);
        }
    }
}
close ($HTML);
[download]

The comments at the top are my workaround, it allowed the script to simply ignore the offending line and continue.
Have fun

   -Etan