For 1.6 I have added an Undo feature to remove ghosts (because Factorio mods can't use the vanilla undo que). First way to use it is clicking the Undo button at the top of the planner UI. The second way it can get triggered is if a new patch selection overlaps with the previous selection.
I looked at the code and noticed it can trigger if there's two patches at the same coords on two different surfaces. Other than that, I'm not sure how it could be misfiring. YARM doesn't seem to have any code that could even order deconstructions. Please report if you notice anything else.