They are eliminated based on the number of chips going into the hand.
So if the 3 players in your example had 100, 200, 300 chips the one with 100 would go out first, the one with 200 second and the one with 300 would be the last to be eliminated.
The guys with the lesser chip will go out first.So if the bubble is only one player away to the money at the time of the elimination of three player with low stack against the big stack who happen to win the hand,then 2 of the eliminated player with better stack will still be in ITM.