JSFiddle - React, Tailwind, and code Playground

HTML

<body>
        <button onclick="myFunction()" id="dif">Difficulty</button>
        <p id="demo">here</p>
        <p id="test"></p>
        <script>
</script>
    </body>

JavaScript

document.getElementById('dif').addEventListener('click',myFunction,false); /*we can't use onclick="myFunction()" on this website, so I used event listener. it is not relevant to your problem..*/

function myFunction() {

      function shuffle(o){ //try this shuffle function
          for(var j, g, t = o.length; t; j = Math.floor(Math.random() * t), g = o[--t], o[t] = o[j], o[j] = g);
          return o;
      };

    var i;    var l;    var y;    var n;
    var newx;   var newy;
    var useranswer;   var amountX;    var largest;
    var copyAmountX;
    var mixAlot;

    var x = parseInt(prompt("What is the first number?"+" "+"(up to 12)"));

    if (x < 13) {
       y = parseInt(prompt("what is the second number?"+" "+"(choose up to 12)")); //**you forgot "parseInt" here
       n = prompt("how many problems to be solved?"); //**you forgot "parseInt" here
       amountX = []; //**you forgot ";"

       // adds to an array equal to x (user input)
       if (!amountX.length) {
        for (var s = 0; s <= x; s++) {
            amountX.push(s);
        }
       };
       // just to let me know if it is working. Will be taken out.
       alert(amountX);
       largest = Math.max.apply(Math, amountX);
       alert(largest);
       alert(isNaN(x));
    }
    else {
        alert("Refresh page and restart with numbers under 12")
    };
    if (y > 12 == true) { //**don't use "== true" if you don't need to
        alert("Refresh page and restart with numbers under 12")
    };

    i = 0;
    l = amountX.length;
    copyAmountX = amountX;
    //**For this to work "newx" has to be outside the loop. and since "newy" and "i" are indentical I will only use "i"
    newx = shuffle(copyAmountX);
    // where the core magic of everything happens.
    while (x < 13 && y < 13 && i<n) { //**you don't need to check if x and y are less than 13, because you don't use them in the while loop
      useranswer = parseInt(prompt("Multiply "+newx+" by "+i)); //**you forgot "parseInt" here....