Sophie got the precious idea in her head that she could grow more rocks for her rock collection by planting them. It seemed like a logical idea and she was so excited that we didn't have the hearts to tell her the truth...right away. So, she planted away.
Then, Clint explained the truth, but also gave her some flower seeds to plant and told her that the rocks in the soil would help her seeds to grow into flowers and he saved the day! Yeah Clint-y!