Let me say upfront that I don't really know. But this is the jist of the conspiracy theory from what I've heard:
They knew that Al Qaeda was planning on attacking the embassy but didn't do anything about it, in fact, they got lax on security measures. Then after it was attacked they denied that it was Al Qaeda and pushed the blame on other stuff, like that 'Innocence of Muslims' movie (or whatever) to keep up the image that Obama was winning the war on terror. Now, after the dust has settled they admit that it was tied to Al Qaeda.
Or something like that, I dunno. I've got better things to worry about.