I had a similar experience whilst kayaking on the Yarra River near Westerfolds Park. Except in this case the rock was real and in the middle of the river. After getting stuck on the rock and damaging my kayak, l returned the next day with a crowbar and moved it to a better position - problem solved. I guess it would be possible to similarly relocate a rock on an orienteering map.
Might be an urban myth but in the days of printed maps a boulder that was there on the ground was missed on a map in the UK for a major event.
Called in the army blew it up
The version of that story I heard involved a Swedish cliff at a 1980s O-ringen.
I can recall some NSW junior squad members removing a boulder from Mohr's Forest by rolling it down a hill. Not sure if it was quite big enough to be mapped or not though.
Around here it's usually that they've been harvested as moss rocks destined for people's gardens - at least the rocks which were taken away mostly weren't big enough to have been mapped individually.
Have experienced the "extra dots on map" during my current mapping activity, using tablet and GPS. Luckily, they appeared in an unmapped section so easy to spot and remove. I think a couple may have popped up when I slipped and fell on a wet, mossy sheet of granite!