Special Values

     for my $row (0..2) {
       for my $col (0..2) {
          print ("<td align=center>" . $squares->[$row][$col] . "</td>\n");
       }
       print ("</tr><tr valign=middle>\n") unless $row == 2;
     }

Now let's fix that ? bug:

     for my $row (0..2) {
       for my $col (0..2) {
          print ("<td align=center>"
                . ($squares->[$row][$col] || "?") 
                . "</td>\n");
       }
       print ("</tr><tr valign=middle>\n") unless $row == 2;
     }

This is a more abstract maxim:
Don't confuse internal and external representations of data