@ danlisa, funny, i have this bug too sometimes, never knew what caused it, but IIRC it also occurs at the next waypoint if it is close (like 5km) to the one deleted.
When navigating under water (mostly when evading DDs) i ususally don't use the plotted course anymore, because of this bug and the follow plotted course makes the engines go to full speed, and hence make noise
if stopped by the telegraph instead of being set to a specific speed