The saveGame command, when used in a script after assigning an objective, appears to cause a glitch where when the next objective is created or assigned etc. the previous objective, assigned before the saveGame, pops up. As well, this re-adds supports and radio communications, if they're added in a script after a saveGame.
This only happens when the player loads the autosave. A clean run through without resorting to a save does not cause this.