Comments on closing brackets can be quite useful for keeping track of flow and bracket symmetry. I went through your sub commenting the closures and the problem quickly revealed itself:

sub setData {
    my($zero) = chr(0);
    my($one) = chr(1);
    my($two) = chr(2);

    open(NDAT,">$path/trivia_dat.cgi");
    foreach $i (0..($n_q - 1)) {
        print NDAT "#";
        print NDAT $INPUT{"q$i"};
        print NDAT "$zero";
        foreach $j (0..($n_a - 1)) {
            if($INPUT{"q$i-c"} eq $j) {
                print NDAT $INPUT{"q$i-a$j"};
                print NDAT "$two"."$one";
            }# if
             elsif($j < ($n_a - 1)) {
                print NDAT $INPUT{"q$i-a$j"};
                print NDAT "$one";
            }# elsif
            else {
                print NDAT $INPUT{"q$i-a$j"};
                print NDAT "\n";
        }# else
    }# foreach
    close(NDAT);
}# foreach
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Oops!