I have 3 Aether portal map markers in my map even though the mod isn't installed. When I remove them they re-appear seconds later.
In the world, there is no glowstone present, not sure what the map is detecting as the portals.

Mind checking what blocks are there? I must have some wrong IDs in the marker

is supplementaries updated?

I'm seeing the same issue on my server as well. Over time, you get like dozens of aether portals.

Supplementaries 1.20 3.1.12
Map Atlas 1.20 6.0.13

That is, indeed, not the latest version

As for the blocks in the area, mostly grass. Sugarcane, water as well but nothing out of the ordinary.

I'm on Supplementaries-1.20-3.1.13
Map Atlases-1.20-6.0.13

Both should be up to date on CurseForge

update supplementaries