You can add a check that the second element has some value.

perl -wle '$a[1]=[1];print $a[1]->[0];if($a[1]->[1]){print$a[1]->[1]}'
r
perl -wle '$a[1]=[1,2];print$a[1]->[0];if($a[1]->[1]){print$a[1]->[1]}
+'
r
l
[download]

something like this should do it in your code

for ( my $i = 0 ; $i < scalar @results ; $i++ ) {
        if ( $results[$i]->[0] eq $disease_name_pocus[0] ) {
            next unless $results[$i]->[1];
            if ( $results[$i]->[1] ne $results[ ( $i + 1 ) ]->[1] ) {
                print MARKER "$results[$i]->[1]\t$results[$i]->[4]\n";
            }
        }
[download]

Cheers,
Random.