The first is the fact that they brought up several times in the season a discussion about how Sam's powers *weren't* coming back, which seems a bit suspicious, and the second is a comment Jared himself made at CreationCon in November, where he indicated that Sam's powers were coming back.

Well, now we know that Sam's powers didn't come back. Yet. :-)

I personally loved the way this was handled, with Ruby giving us hints that Sam's powers are still there and then Lilith unable to kill Sam. I'll be perfectly happy now if Sam taps into those buried abilities next season to save Dean. But I don't want him to go Darkside for too long!