I think the restoring everyone to the right timeline could be the "incident". I think it makes since the Swann is directly affected by this "incident" because with it's destruction it sent Desmond tripping through time. Faraday has experience through his experiments and combined with his Dharma notes it is conceivable he could subversively build the Swann to be a time machine.

Or possibly the incident could have already been hinted at in one of the training videos. Do you remember the Orchid training video with the rabbits? Possibly someone meets themselves and something catastrophic happens.

Ever since we saw Jughead (the H Bomb)hanging by a thread back in the 1950's, I always wonder if a leak or some other accident with Jughead might've been the incident. I don't have much to back this up, but it's something to ponder.

I'm sure a Jughead centric storyline will reappear at some point in future episodes. It would be too random for them to introduce an H Bomb in one episode and then never feature it ever again.

This is what we think we know about the incident:

It happened after Jughead in 1954.
It happened after the Hostiles & Dharma were introduced to time leapers in 1977.
It happened after Faraday showed up in 1977. Faraday, who happens to be a. The son of Hawking and b. A time travel experimenting scientist.
It happened before Radinzsky's suicide and so it happened before Desmond's button pushing began. So it seems possible (probable?) that the button pushing is a direct result of the Incident.

Then when the button wasn't pushed, 815 fell out of the sky. Then Desmond averted we don't know what by turning the fail safe key and Desmond began time traveling. Then the FDW was turned by Ben and time looping began for the 815ers. Then Locke turned the NotFDW and time looping ceased.

So it seems reasonable to entertain the possibility that Faraday introduced the ability to time travel to Dharma and that is what caused The Incident.

Because...what happened happened. You can't change it. Which might mean that you can in fact change it, but you must not change it. That makes sense. The fact of the matter is that if you go back in time, you have absolutely changed what happened.

It might be that what we are watching are attempts to mitigate the damages done by people who screwed with time before they knew its far reaching consequences.

Sort of like we are, in real life, trying to mitigate the damage to humanity by people who screwed with atom splitting before they understood the far reaching consequences.