So maybe, they tried to in the last minute find a safe place for Kushina to give birth, because Tobi somehow got spotted, Kushina had a hunch or [insert plot device].
Somehow, they stumble into grouchy just woken up Horo [or other being], and in resulting chaos seal her into Naruto.
That however possibly butterflies Naruto's parents being dead, so not sure if not to much subplotting.