This is barely a feature and almost a bug.
In most of the directories there are index.php files intended to push the random user that tries to access these directories directly up one level until it reaches the board index.
Nice idea... in theory.
Most of the times I have seen this in action is when an image or a script or something is missing and the fallback loads the board index causing load (it's equivalent to load two or more pages at one) and mess (I just had a darn session issue because of that).
What do you think of an htaccess that just prohibits the listing of files (should be possible) instead? Or an empty index.html?