Solution with (a little)more output data, feedback appreciated.

// Variables
var answer;
var answers = [[], []];

// Array with questions and answers
var questions = [
    ["How much is 2+2?", "four"],
    ["Sky color?", "blue"],
    ["Worst programming language?", "php"]
];

// Put the content inside the #output div withouth erasing the previous data
function print(message) {
  var outputDiv = document.getElementById("output");
  outputDiv.innerHTML += message;
}

// Build a proper html list from an array
function buildList(list) {
    var listHTML ="<ol>";
    for(var i = 0; i < list.length; i += 1) {
        listHTML += "<li>" + list[i] + "</li>";
    }
    listHTML += "</ol>";
    return listHTML;
}

//Ask questions=[i][0] and save wrong/correct answers
for (var i = 0 ; i < questions.length ; i += 1) {
        answer = prompt(questions[i][0]);
        // If correct, store question and answer in the first array inside answers=[[correct answers],[]]
        if (answer === questions[i][1]) {
                alert("Correct!");
                answers[0].push(questions[i][0] + " R: " + answer);
        // If wrong, store question, wrong answer and correct answer in the second array inside answers=[[],[wrong answers]]
        } else {
            alert("Wrong!");
            answers[1].push(questions[i][0] + " Your answer: " + answer + " Correct answer: " + questions[i][1]);
        }
}

//Print the lists with correct and wrong answers
print("<h2>You got " + answers[0].length + " correct answers:</h2>" + buildList( answers[0] ) );
print("<h2>And " + answers[1].length + " wrong answers:</h2>" + buildList( answers[1] ) );