Not sure if this goes to you or not, but when you click on the Episodes tab and mouse over Season 1, there are a few of episodes missing from the list: Murphy's Law, Twilight's Last Gleaming, Day Trip, and I Am Become Death are all missing from the list. Season 2 is also missing the last 6 episodes.
I am no quite sure where you are referring to exactly. However, I believe you are referring to the drop lists for season 1 and season 2 on the navigation bar.
Unfortunately, the navigation bar only allows 10 links per drop down. Because of this, the top 10 highest ranking episodes from Season 1 are displayed. Season 2 we went until mid-season. Eventually, this list will be updated with the top 10 highest ranking episodes from Season 2.
You will also notice under characters, it is the same thing. We only display a max of 9 per drop down and then a link to all the rest of the characters for that category.