Create a gamelogic and give it a set of waypoints. Place one waypoint inside the area of each trigger in the mission. Synchro the last waypoint (which most NOT be in a trigger area) to all other waypoints in the game. Name the GL bugfix. Preview the mission, SAVE IT and then delete the GL.
Look over the mission and check that nothing untoward has happened: this is useful tool embedded in the game, not a magic wand that miraculously knows what you are trying to do. There is apparently a log file created somewhere but I've never found it. For that reason it is better to run this regularly rather than just when the mission is ready for beta testing, so that you can keep track of what is happening.
It's helpful to put a hint in the last of its waypoints so you know it has got there successfully and fixed all the bugs, it can take a few minutes. Obviously it won't fix bugs in scripts or in triggers that have no area. Remember to give the GL maximum skill.
If you want it to fix bugs in init lines then group the GL with the group rather than giving it waypoints. It can't be group leader and its a slightly tedious business because it can't override the maximum of 12 in a group, so you basically have to do it for each group individually.