I'm guessing that this will be one of the things that will be answered pretty quickly in Season 6. When Locke, Sawyer and co were going through the flashes they were chased in the other outrigger by an unknown party. We can deduce from the Ajira bottle in them that it must have been from post-2007 316 crash, so I was thinking about who these people will be.
I think this, along with other things that were recently set up, show that there won't be a reset as it would have been very random to not explain it. It could be Jack & co time travelling back to the correct time, but I wouldn't think they would randomly shoot at the other boat, and where would they get a gun from?
I'm thinking its most likely going to be Caeser. It won't be Ilana/Bram and co because they've already go to where they need to be and didn't need the boat as far as I know. I'm guessing, much like Lost in the past, people don't just die when you expect they would (Locke being shot by Ben, Mikhail with the fence/harpoon gun). Even though the idea of Caeser being set up as a big character to then just be shot straight away seemed interesting as it did what they intended to do with Jack at the very beginning, I reckon he'll turn into a semi-important character. From re-watching it seems he may just be a simple passenger like our losties, who's just very good at what he does (like Sayid, Jack, Locke etc). For me, it seems he doesn't know Ilana because when they crashed he helped her up calling her 'lady', so I reckon he won't be anything important in the same way that Ilana & Bram are, in that they intended to get there also. I think he may just be a passenger, but like our losties, is there for a reason.
And so I think after he was shot by Ben, he will have survived for some reason (rubber bullets/healed by island/shot in place like Locke). And so he and the rest of the normal passengers (there are still a few left), got pissed and scared that these guys have been to the island before (shot by Ben, and then Ilana and co went off with guns and a crate), and so took the other outrigger when they discovered the other one had been taken. They catch up to it, thinking its either Ben or Ilana, and for them, quite rightly shoot at them, for they believe them to be hostile, or others! And so the whole thing starts over. However, as we know, its just Juliet & co skipping through time. One of them will get shot by her, get confused when they vanish, and go to shore and catch up with Frank & co.
For me, this is the only explanation to the outrigger chase, and will be cool if Caeser actually had a point :)