Well, things seem to be pointing toward Miles also being born on the island...
Perhaps he is Pierre's baby that we saw in the Season Five opener?
Juliet had been on the island for around three years I believe it was said, and since she was the last person to get nosebleeds I guess that means Miles must have been on it for longer than that before. Definitely leaning toward him being the baby...
I believe the jump with Ajira was in the future. I wouldn't be surprised if the people chasing them/shooting at them were the O6. I get the feeling that in order to get back to the island, the O6 and Ben use another airplane and crash (or perhaps land... there's always that runway that was being built on the Hydra Island to consider...) and they obviously use Ajira. So, yeah, I wouldn't be surprised if it was revealed to be them later down the road.