To undo a player's bust-out, either press the "F" key (just above the "V" key used to rebuy players), or press the "Undo Rebuy" button on the Controls tab.
After the fact, go to the Players tab and edit the player (double-click the player). Then, in the Tournament History section, right-click on the "Rebuy" line and select "Undo rebuy". This should also undo the final bust-out that you had to do to get the player out of the tournament.