Your site looks like this:
<div class="navbar-header" style="position:absolute; z-index:2;">
<button type="button" class="navbar-toggle" data-toggle="collapse" data-target=".navbar-collapse">
<span class="sr-only">Toggle navigation</span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
<a class="navbar-brand" href="index.html"><img src="images/logo.png" alt="logo"></a>
</div>
Change position: absolute
to position: relative
It will fit according to the Layout, in the way that you require the image to stay there regardless of what happens to the page.
It will look like this:
<div class="navbar-header" style="position:relative; z-index:2;">
<button type="button" class="navbar-toggle" data-toggle="collapse" data-target=".navbar-collapse">
<span class="sr-only">Toggle navigation</span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
<a class="navbar-brand" href="index.html"><img src="images/logo.png" alt="logo"></a>
</div>