The first image is from IE9 and above, while the second one is from IE8. In IE8, the right side goes down because it's displaying in mobile view (Check the top menu)
Here is the header code I am using:
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<!-- HTML5 shim and Respond.js IE8 support of HTML5 elements and media queries -->
<!--[if lt IE 9]>
<script src="https://oss.maxcdn.com/html5shiv/3.7.2/html5shiv.min.js"></script>
<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
<![endif]-->
And this is how I am structuring my layout:
<div class="container">
<div class="col-md-9 col-sm-8">LEFT</div>
<div class="col-md-3 col-sm-4">RIGHT</div>
</div>