I'm guessing that's one of the island's mysteries . . . how time passes . . . I think their basically in a different dimension. It kinda explains why u have to be at a certain compass bearing to reach the island, kinda like a wormhole . . . now I'm no scientist but that's what I'm guessing.
Its not like an unexplained time gap on the writer's part, because Aaron aged, so the 3 years definately passed (off the island), but they have been experiencing time flashes so they dont know how much time really passed (now that I think of it, thats probably why, lol).