You may also need to keep digging until you find six "Chocograph Pieces," which will allow you to upgrade Choco to the golden color. I wonder if that's why you can't dig up anymore. If Mene is saying that you've found all the Chocographs in both the Lagoon and the Forest, you need to work on finding Chocobo's Air Garden.

For that, you'll need to find all six chocograph pieces, which will give you the "Mist Ocean" chocograph. With that, you get Choco upgraded to gold, and then you can find the Air Garden and the last few chocographs.