Bootstrap putting checkbox in a dropdown

I'm trying to put a checkbox form in a dropdown like this:

<ul>
  <li class="dropdown">
    <a href="#" data-toggle="dropdown" class="dropdown-toggle">
      Dropdown Form<b class="caret"></b>
    </a>
    <ul class="dropdown-menu">
      <li><label class="checkbox"><input type="checkbox">Two</label></li>
      <li><label class="checkbox"><input type="checkbox">Two</label></li>
    </ul>
  </li>
</ul>

Here is a Demo in Bootply

However, as you can see in the demo, for whatever reason the actual checkbox itself appears outside of the dropdown menu. Can anyone tell me what's causing that, and how it should be implemented instead? If I take the label class out it works but it's all bunched up.

Here's what we'll build:

HTML

Essentially, we'll look to combine two different sets of Bootstrap controls & styles: Dropdowns & Checkboxes. Inside of each li, we'll use a label instead of an a element, so that we can wrap the checkbox in a label and make the entire row clickable.

<!-- language: lang-html -->

<ul class="dropdown-menu checkbox-menu allow-focus">
  <li >
    <label>
      <input type="checkbox"> Cheese
    </label>
  </li>
</ul>

CSS

We can steal some of the styles normally applied to .dropdown-menu li a, input and apply them to our label option instead. We'll make the label occupy the full width of the container and fix some label / checkbox alignment issues. Additionally, we'll add styles for .active and :hover.

<!-- language: lang-css -->

.checkbox-menu li label {
    display: block;
    padding: 3px 10px;
    clear: both;
    font-weight: normal;
    line-height: 1.42857143;
    color: #333;
    white-space: nowrap;
    margin:0;
    transition: background-color .4s ease;
}
.checkbox-menu li input {
    margin: 0px 5px;
    top: 2px;
    position: relative;
}

.checkbox-menu li.active label {
    background-color: #cbcbff;
    font-weight:bold;
}

.checkbox-menu li label:hover,
.checkbox-menu li label:focus {
    background-color: #f5f5f5;
}

.checkbox-menu li.active label:hover,
.checkbox-menu li.active label:focus {
    background-color: #b8b8ff;
}

JavaScript

Some other housekeeping, we'll manually keep an .active class flag on each list item to correspond to whether or not the item is checked so we can style it appropriately.

<!-- language: lang-js -->

$(".checkbox-menu").on("change", "input[type='checkbox']", function() {
   $(this).closest("li").toggleClass("active", this.checked);
});

We'll also want to allow multiple selections by allowing the menu to stay open on internal click events by stopping the event from bubbling up

<!-- language: lang-js -->

$(document).on('click', '.allow-focus', function (e) {
  e.stopPropagation();
});

Demo in Stack Snippets

<!-- begin snippet: js hide: true console: true babel: false --> <!-- language: lang-js -->

$(".checkbox-menu").on("change", "input[type='checkbox']", function() {
   $(this).closest("li").toggleClass("active", this.checked);
});

$(document).on('click', '.allow-focus', function (e) {
  e.stopPropagation();
});

<!-- language: lang-css -->

body {
  padding: 15px;
}

.checkbox-menu li label {
    display: block;
    padding: 3px 10px;
    clear: both;
    font-weight: normal;
    line-height: 1.42857143;
    color: #333;
    white-space: nowrap;
    margin:0;
    transition: background-color .4s ease;
}
.checkbox-menu li input {
    margin: 0px 5px;
    top: 2px;
    position: relative;
}

.checkbox-menu li.active label {
    background-color: #cbcbff;
    font-weight:bold;
}

.checkbox-menu li label:hover,
.checkbox-menu li label:focus {
    background-color: #f5f5f5;
}

.checkbox-menu li.active label:hover,
.checkbox-menu li.active label:focus {
    background-color: #b8b8ff;
}

<!-- language: lang-html -->

<link href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/css/bootstrap.css" rel="stylesheet"/>
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js"></script>
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.js"></script>



<div class="dropdown">
  <button class="btn btn-default dropdown-toggle" type="button" 
          id="dropdownMenu1" data-toggle="dropdown" 
          aria-haspopup="true" aria-expanded="true">
    <i class="glyphicon glyphicon-cog"></i>
    <span class="caret"></span>
  </button>
  <ul class="dropdown-menu checkbox-menu allow-focus" aria-labelledby="dropdownMenu1">
  
    <li >
      <label>
        <input type="checkbox"> Cheese
      </label>
    </li>
    
    <li >
      <label>
        <input type="checkbox"> Pepperoni
      </label>
    </li>
    
    <li >
      <label>
        <input type="checkbox"> Peppers
      </label>
    </li>
    
  </ul>
</div>

<!-- end snippet -->