When i used code formatting in latte file, then HTLM and CSS was been formatted correctly but javascript was been shifted, as you may seen on example.
Exist one solution, what i know. Remove the initial javascript tag, run automatic formating (javascript code will be moved to left), insert back initial javascript tag and run automatic formating. At the moment, the code will be formatted correctly. But when we will use formating again, the code will be shifted.
When i previously was using Netbeans version 6.2, the code formatting worked correctly
Example:

{literal}
--HTML over javacript--
<script type="text/javascript">
                $(function() {
        $(".ajaxPermission").off("click").on("click", function()
        {
            var id = $(this).attr("data-id");
                        var status = $(this).attr("data-status");
                        //Do somethings
                    });
                    $(".resourceName").off("click").on("click", function() {
                        var bullet = $(this).find(".toggle");
                                    var data = $(this).parent().children(".resourceData");
                                    if (bullet.hasClass("icon-bullet_toggle_plus"))
                                                {
                                                                        bullet.removeClass("icon-bullet_toggle_plus").addClass("icon-bullet_toggle_minus");
                                                                                        data.show();
                                                                                    } else {
                                                                            bullet.removeClass("icon-bullet_toggle_minus").addClass("icon-bullet_toggle_plus");
                                                                                            data.hide();
                                                                                        }
                                                                                    });
                                                                                });
</script>
--HTML below the javascript--


Product Version: NetBeans IDE 7.4 (Build 201310111528)
Updates: NetBeans IDE is updated to version NetBeans 7.4 Patch 2
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