This is a well known problem with bootstrap:
If you use a fixed navigation bar at the top, whenever you follow a link to somewhere inside the page, the actual link target is going to be hidden below that freaking navigation bar.
There are a ton of solutions, which have two tons of minor issues. There seems to be no way to solve this using CSS and JS without causing other problems.
There are a bunch of JS solutions around. Here's mine:
It works well, is short and has decent browser coverage. It only fails in the corner case of clicking on the same internal link twice (which, who cares).