In the part where you have to solve the boulder puzzle, I accidentally dropped the first boulder in to the wrong hole(The one to the left of the boulder). Is there any way I can undo this action? I do not have a savestate before this happened.
You can leave the area then come back, OR save and reload the game. Both ways the boulders will be back to their original positions.
If i recall correctly speaking to one of the lake trio (Uxie, Azelf or Mesprit) nearby will reset the puzzle you are currently doing