I think the time thing is throwing everything off. When the wraith comes into FTL, it goes after Philip. Mary Margaret and Emma came in at the same time, but are left in the wreckage. Then, the rest of the FTL story starts. Technically, most of what we saw in FTL was a flashforward. We just didn’t know it until the end of the episode.
That does make a lot of sense. My only issue with this is it means that Emma and Snow were unconscious in the wreckage for more than a day… you would think they would have woken up before then…