Thoughts? I am sure this could be more efficient, but I tried to add safeguards for number/letters answers.

var quiz = [
 ["What color is a fire truck?", "red"],
 ["How many legs does a cat have?", "4"],
 ["What is 1 + 2?", "3"] 
]

var rightQuestions = [];
var wrongQuestions= [];
var score = 0;
var wrong = 0;
var newAnswer= "";
var htmlMessage = "";
var wrongOnes = "";
var rightOnes = "";
var wrongOnesHTML = "";
var rightOnesHTML = "";



function print(message) {
  document.write(message);
}


function ask(question){
 var  answer = prompt(question); 
 return answer;
}

//Goes through array to create questions for test
function buildList(questions){
 var list = "";
 list += "<ul>";
 for (i=0; i < questions.length; i+=1) {
  list += "<li> " + questions[i] + "</li>";    
 }
  list += "</ul>";
  return list;
}

//Allows user to enter "three" and "four" for "3" and "4" and still get correct
function cleanUpAnswer (item){ 
  if (item === "three"){
    item = "3";
  }else if(item === "four"){
      item = "4";
  }
    return item;
}


// Take The Test; Determine what to do with right and wrong questions

for (i=0; i<quiz.length; i+=1) {
 answer = ask(quiz[i][0]);
 console.log(answer);
   newAnswer = cleanUpAnswer(answer.toLowerCase());
   console.log(newAnswer);
 if (newAnswer === quiz[i][1]){ 
   console.log ("Correct!");
   score +=1; 
   rightQuestions.push(quiz[i][0]);
   console.log(rightQuestions); 
 }else {
    console.log ("NOT Correct!");
    wrongQuestions.push(quiz[i][0]);
    console.log(wrongQuestions); 
 }

}
console.log(score);
wrong = wrongQuestions.length;
//Create the Final Score and Lists
htmlMessage = "You got " + score + " correct, and " + wrong + "  wrong!";
wrongOnes = buildList(wrongQuestions); 
rightOnes = buildList(rightQuestions);
wrongOnesHTML = "<h1>You Got These Questions Wrong</h1>";
rightOnesHTML = "<h1>You Got These Questions Right</h1>";


// Print Out the Final Score and Lists
print(htmlMessage);

//Don't show right or wrong questions unless there is something in array
if (wrongQuestions.length > 0){
print(wrongOnesHTML + wrongOnes);
}
if (rightQuestions.length > 0){
print(rightOnesHTML + rightOnes);
}