Posting on Whedonesque.com, the writer explained why there was confusion, and set the story straight.
“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 we go.
No cancellation, yet, and that’s the 13th episode explained.