Mark a POI as visited

According to this Polygon article, (be warned, there may be spoilers if you read too far into the article) following the Atlas Path will bring you along to more Atlas Interfaces/Space Anomalies. This will allow you to get the stones you need.

However, in your specific case, finding one after straying from the actual path, and without Nada and Polo's help, is really up to chance. As far as I can tell, you'll just need to keep flying through new systems to find a new Atlas Interface. This is just a slight speculation based on what I've dared to read in the article, and from my own experience. I don't want to spoil the game for myself, what with all the information and mystery surrounding the center of the galaxy so unfortunately this is the best I can do.

As it stands you are no longer able to do the Atlas quest as leaving the final station makes it stop existing, meaning that you cannot complete it.

This has been an issue since launch and it appear that it has not been addressed in any of the patch notes on the official website for the game.

The issue was documented by a few different people such as Escapist writer Shamus Young and Forbes writer Paul Tassi. The articles are pretty negative but talk about having the same problem that you are having under the same circumstances.