It looks to me like the 'arrived at waypoint' is triggering as the plugin calculates the path ahead of the object's movement position. But, further tests show that it does
trigger twice near the correct spots, by spawning another sprite instead of destroying the markers. Anyway, if I quickly place a long series of waypoints ahead of the sprite, they disappear long before it's movement finishes, but it does complete the path correctly.
I'd say that this is probably unintended behavior, and thus a bug. You may be able to work around it with a proximity check (the object is not guaranteed to overlap them,) and a queue of waypoints (to ensure that they are destroyed in order when paths overlap.) This would not be easy.
Perhaps an acceptable alternative can be implemented, such as simply having each waypoint fade away after a certain amount of time, or leaving them all until the final destination is reached, then destroying all of them.EDIT -
Removed flawed workaround, to prevent confusion. R0J0hound posted a good one below. Nice one, R0J0hound!