This program's bookmarklet, khanacademy.org/cs/i/6347724702416896, ported to TamperMonkey. Still quite buggy and doesn't always work.

EytukanTamperMonkey.js

// ==UserScript==
// @name         Show flags on programs
// @version      1.1
// @description  Shows number of flags for a program, even on the hot list (khanacademy.org/cs/i/6347724702416896)
// @author       Eytukan (ported by Matthias)
// @match        https://www.khanacademy.org/computing/computer-programming/browse
// @match        https://www.khanacademy.org/profile/*/projects
// @grant        none
// ==/UserScript==

(function() {
    'use strict';

    console.log("Hello");

    var programLinks;
    var id, counter, ids, objs, result;
    var interval;
    var getJSON = function(url, callback) {
        var xhr = new XMLHttpRequest();
        xhr.open('GET', url, true);
        xhr.responseType = 'json';
        xhr.onload = function() {
            var status = xhr.status;
            if (status == 200) {
                callback(null, xhr.response);
            } else {
                callback(status);
            }
        };
        xhr.send();
    };

    function handleResponse(data) {
        ids.push(parseInt(programLinks[counter].href.split("/")[5]));
        objs.push(data);
        if ( counter === programLinks.length - 1 ) {
            result = objs.sort(function(a,b){
                return ids.indexOf(a.id) < ids.indexOf(b.id) ? -1 : 1;
            });
            for (var j = 0; j < result.length; j++) {
                programLinks[j].nextSibling.nextSibling.innerHTML +=  " · " + result[j].flags.length + " Flag" + (result[j].flags.length === 1 ? "" : "s");
            }
        }
    }

    function init() {
        programLinks = document.getElementsByClassName("link_1uvuyao-o_O-noUnderline_4133r1");
        counter = 0;
        ids = [];
        objs = [];
        if (programLinks.length === 0) {
            console.log("Failed to find programs");
            return;
        }
        window.clearInterval(interval);

        var buttons = document.getElementsByClassName("sorts_1l7kz3k").childNodes;
        for (var i = 0; i < buttons.length; i++) {
            buttons[i].addEventListener("click", function () {
                interval = window.setInterval(init, 500);
            });
        }

        for (var i = 0; i < programLinks.length; i++) {
            id = programLinks[i].href.split("/")[5];
            getJSON("https://www.khanacademy.org/api/internal/scratchpads/" + id, function(err, data) {
                handleResponse(data);
                counter++;
            });
        }
    }

    interval = window.setInterval(init, 500);
})();