There was a lot of hullabaloo over Dollhouse recently, after Buffy actress Felicia Day "twittered" that Fox aren't going to air the thirteenth episode ("Epitaph One") that she guest-stars in -- meaning the season will conclude with episode twelve ("Omega"). Dollhouse writer Tim Minear then clarified the situation at Whedonesque.com:
"Okay. So maybe I can help clarify this somewhat. Because we scrapped the original pilot -- and in fact cannibalized some of its parts for other eps -- we really ended up with 12 episodes. But the studio makes DVD and other deals based on the original 13 number. So we created a standalone kind of coda episode. Which is the mythical new episode 13. The network had already paid for 13 episodes, and this included the one they agreed to let us scrap for parts. It does not include the one we made to bring the number back up to 13 for the studio side and its obligations. We always knew it would be for the DVD for sure, but we also think Fox should air it because it's awesome."
So, there you have it from the horse's mouth. "Epitaph One" isn't written as a season finale, but has been produced outside of the 13-episode agreement with Fox. I suspect it will appear on the Dollhouse DVD as a "bonus unaired episode", then perhaps show up early in season 2. If the series gets renewed, of course.