Rocks

I noticed that, also. Inside (once you beat Groudon) you can dive in one spot in the rapids west of Pacificdog Town. Once you find that spot (It takes forever), go under (make sure you have a Wailmer in the back of your party, and a Relicanth in the front)go to the dots on the wall (braille) and use dive. You will be in another room. Go to the braille on the farthest stone, use dig. :message: "3 doors opened far away". The three rock formations like that will have a door on them. One of them, you have to stand in the center of the room and use fly. One, you have to move 2 down from the braille and 3 right (or opposite, may not be perfectly accurate) and use strength. The last, you have to read the braille. Inside the caves that open when you do one of these things (one for each cave, but I don't know which task corresponds with which cavve) you will battle Regirock, Registeel, and Regice.

Ah, yes, I do think that I know what you are talking about. You see, there is one more spot like that, and they contain something very nice inside. In every one of these strange rock foundations...lies a legendary Pokemon that is waiting for you to catch him! That means that you can get Three new Pokemon added to the Pokedex, and get three new legendary Pokemon. I could tell you how to get there, but it would not be descriptive enough. I suggest that you look on youtube.com for a video on how to catch the regi's. However, you need to have a Wailord, and a Relicanth. Hope this helps.

There are 3 places like this

These are where regice, registeel, and regirock are.

To get in you first need to go to an underwater cavern somewhere between lilycove and slateport. You also need a relicanth, a wailord, a Pokemon with dig and a Pokemon with dive. The instructions are written in brialle on rocks.

What you find was the three regis homes(regice, regirock, registeel)

Those rocks are the places in which the Regi's lie dormant. (Regice, Regirock, Registeel)