Is it possible to get more Atlas Stones?

As far as I know, Atlas Stones can be received from Atlas Stations you find along your exploration. You can find them randomly, or they will likely be on your specific path to the center of the universe.

As to getting them randomly from around the systems and planets, I want to say no. However, you can buy them from some traders, albeit extremely overpriced (5+ Million Units).

Some traders will have Atlas stones for sale. So far I personally have only seen a few for sale at space stations. They are usually a couple million units each. I suspect you would have to shift paths to free explore, earn many units, and find more stones before you can continue back on to the goal that needs those stones.