Found that this still happens with factorio 1.0 for some reason for me, and couldn't really find anything about why it happens, aside for couple similar reports with biter dots are "freezing" on the map in various cases.
Map dots that such non-unit wisps leave seem to disappear when they get replaced by new ones somewhere else, so not very serious issue, more like a quirk.
Ended up using a workaround with map_color = {r=0, g=0, b=0, a=0} to make these things transparent on the map, but weirdly enough factorio still draws faint dark-ish pixels for them even with alpha=0, and these do get left behind same as bright red ones before, just way harder to notice, unless one is looking for them.
