I picked up on 3 seemingly throw away lines that I think may shed some light on what is going on:
From LA X - BERNARD: Now I know how the laundry feels when it's in the dryer
From What Kate Does- DOCTOR GOODSPEED: [to nurse 2] Margaret, let's do an ultrasound. I wanna get a picture of what's going on in there. [to Claire] Ah, it, it could just mean the baby's out of position.
DOCTOR GOODSPEED: See? [chuckles] There he is. Everything is just fine. [Monitor returns to beeping.] Your boy just likes to move around.
For the Substitute - BEN: Alright, I know I sound like a broken record, but how many times do we have to go over this? If you have the last cup of coffee, you remove the filter and throw it away. Fear not. I will make a fresh pot.
The Comments from Bernard and Ben I believe are there as a wink and a nod to what is going on. The dryer spins the clothes around and around and the broken record keeps skipping back over the same section over and over. I believe there are multiple time lines that are playing out. I also believe that the LA X alt is actually a composite of multiple time lines. The events are playing out over and over until everyone is in the right place. This would explain why in What Kate Does we are seeing Oct. and in the Substitute is it sometime before Oct. There are slightly different time lines.
The Goodspeed comments on Aaron are particularly interesting. I think when he says that Aaron is out of position, he is actually saying that Aaron is not there. He follows that up by saying Aaron likes to move around. I believe that Aaron is skipping around to various alt time lines. Similar to what Desmond or the on island people experienced. I am not sure if he has control of it or not. I think the boy in the jungle may be an older Aaron that is moving around in time. It may be that Jacob is also Aaron. This would explain his ability to travel back in time and touch the various people. It would also explain why Aaron seemed to disappear in the O6 world.