Damn you, Bourne.

It's entirely possible they time travel in the new timeline, and continue to want to set off the bomb, and do.

- How would Juliet know?
- Were there any little clues or inconsistencies in the on-island scenes tonight to suggest any past events have changed?
- Can you think of any other way to tie these two timelines together without resorting to some deus ex island mumbo jumbo?

"It worked."
This implies to me that maybe the presumed "alternate timeline" we're seeing isn't alternate at all. That we're seeing flashbacks to the new timeline created by the bomb, and that those flashbacks will eventually lead to the characters finding their way to the island and back into the same predicament…

Wilco, "The Late Greats"
Just sayin'.