I've considered that; but take note of a few things: They did come from the Hydra island, so the closest dock should be the Pala Ferry, right? EDIT: No I guess this one isn't true as the dock didn't have the Pala Ferry sign on it and was shaped differently. Also the other island wasn't visible from the Pala Ferry dock. Also the barracks is surrounded by the sonic fence, and is not close to the shore, as seen on the map in season 3 that they pulled from the flame before lock blew it up. As far as the sub is concerned, we saw in this episode even, that the new recruits are delivered to the barracks from the sub in the Dharma van, so it is clearly far enough away to require a vehicle. I may be completely barking up the wrong tree here, and these items may just be oversights by the writing/editing team, but I'm just sayin'.