The official line from E! is as follows:
OK, brace yourself, guys, because there’s going to be math in this story.
Fox the television network will not be airing the "13th episode" of Dollhouse. However, there appears to be some debate about what qualifies as a 13th episode and what qualifies as a season finale.
Fox the television network ordered 13 episodes of Dollhouse. As everybody knows, they scrapped the original pilot, "Echo." So that is 13 less one, which brings us down to 12. The 12th and final episode that Fox the television network ordered and paid for and will air is called "Omega," was written and directed by Tim Minear (who has told us he "can’t wait" for us to see it). Focused on the Alpha storyline, sources say that "Omega" apparently "closes some doors and opens other ones," and was always intended to be and serves effectively as the season one finale.
Now, let’s go back to the equation, and add in a episode called "Epitaph One." "Echo" the original pilot + 12 episodes through "Omega" + "Epitaph One" brings us to a total of 14 episodes.
The 14th episode, "Epitaph One," was produced and paid for by Fox the television studio. It was not ever ordered/requested/paid for by Fox the television network, and Fox the television network will not be airing "Epitaph One." Working on getting you more details about "Epitaph One," but it’s said to be more of a "standalone" episode.
So, to summarize, Fox the television studio made 14 episodes of Dollhouse, and Fox the television studio is airing 12 of them, and paid for the 13 that they originally ordered.
A last, and very important note: According to sources on the network side, them not picking up and airing "Epitaph One" has no bearing whatsoever on whether or not they pick up the series for a second season, a situation which, I’m told, is "100 phase in the decision phase." You can obviously believe them or not as you choose, but I take them at their word. I may be a sucker like that.
Felicia Day has also semi-retracted her claim on Twitter, now posting:
Psh what a can of worms! E Online clarifies: Dollhouse is NOT cancelled, Ep #13 is confusing, I’m gonna go write now :)
Things are never simple with FOX, are they? They can’t even cancel something expectedly anymore, they have to do it the hard way.
More heartache for the fans out there. Clarification is always welcome, if not often forthcoming from the American network.
Time will tell. Still don’t see it getting picked up for a second season with its current ratings. This final episode thing is probably merely a technicality. And besides, I’ve heard some nonsensical mumbo-jumbo in my time, but if anyone can explain to me what "100 phase in the decision phase” means, then you’ll receive a free Sands of Oblivion DVD.