I am trying out twitter bootstrap and am new to CSS/HTML. Here’s my simple HTML:
<!DOCTYPE html>
<html>
<head>
......
</head>
<body>
<div class="navbar">
<div class="navbar-inner">
<div class="container">
<a class="brand" href="#">Test App</a>
</div>
</div>
</div>
</body>
</html>

check in firebug, either of your container –
navbar, navbar-inner, containermay havepaddingormargin.