There are all sorts of weird issues with how the game updates the terrain visuals when you gather resources that change it. For large mineral veins it will update the terrain when you're close but shift back to the pre-mined terrain once you move further out; in both cases the game engine knows that the resource is gone, so what's it's showing is not a reflection of the actual game state. For the one-off gatherables like Vortox Cubes, Albumen Pearls, Aquaspheres etc it does the exact same thing - if you gather in an area and then double back the resource nodes will still be there but under the hood the resources themselves are gone. It's quite maddening when you're doing big gathering loops since (of course) you also have no way to mark territory that you've already been through on any kind of map and the terrain all looks the same. It sounds like in the case of the vortex cubes it's attempting to "hide" them once they've been gathered but not actually removing them from the terrain.
The entire planetary surface system is hilariously janky. Have you noticed that if you stand in one place and "scan" you'll pick up different random things around you every time? It's like the scanner just picks objects at random to identify from a list of whatever is close by.