Well, no map making master am I....but I have also had the same problem, mostly when i put an addon on a map, then after awhile, think better of it and delete it. This, is of course, usually after I have saved it a million times, so tha addon still shows in the sqm file. Here is what I have found to fix it.
Open the map in the editor
put a box around EVERYTHING you placed on the map
hit cntrl X to cut everything
close the editor
open the editor to the island you want your map to take place on
find the correct placement for a "paste"
hit cntrl V to paste everything you cut from the previos map
(be sure to have a reference point for your mouse when cutting, like a numbered hilltop, it make pasting it all back much easier)
now, save the mission as PASTE or something simple, alt/tab out, go to your missions folder and open the sqm file, all the "ghost addons" should no longer be present
then simply delete the map pbo from the MPMissions or Missions folder, depending on what kind of map it was, copy all the sqs files from the original map folder, making sure to leave the mission sqm file, and put them in the new pasted map folder. Delete the original folder, go back in editor and save map again, export it, and give it a whirl.
Not to sound like a sneak or anything.......but i have also used this method when placing maps on the server that has a ghost addon, these are other ppls maps, but i never change their map in any way, shape or form, I only do it if there is an addon problem on our server.