If you're not tracking players, this shouldn't be an issue. So I will assume you are.
There are two ways, off the top of my head, to "fix" things when players fail to alert the TD that they've busted out.
1) Edit the player on the Players tab, and in the Tournament History section, insert a bust-out at the appropriate place/time
2) Bust all remaining players out of the tournament, and then use the "Adjust Rankings" feature (button) on the Players tab to move players into their appropriate bust-out position
This will take care of rankings, which takes care of points and prizes for you. How are you accomplishing this today and which part is the tedious part?