First new post and embedded tweets
When you click on a previously read thread and go to the first new post, any embedded tweets on that page mess up the positioning and leave you looking at posts higher up on the page. I think what's happening is that the page loads, the browser goes to the appropriate location, and then the tweet links get turned into embedded tweets that push everything below them down the page. If there are a lot of separate or quoted tweets you can end up several screen lengths away from the first new post.
One thread that has this problem crop up frequently is here