Beraishis

As we read of the creation of the world, the posuk tells us ויאמר אלקים תדשא הארץ דשא עשב מזריע זרע עץ פרי עשה פרי למינו אשר זרעו בו על הארץ ויהי כן

Hashem said, "let the earth sprout vegetation of plants bringing forth seed, trees of fruit yielding fruit each after its kind, which have their seed in them on the earth." And it was so.   

Rashi says that the flavor of the tree shall be the same flavor as the fruit.  
However the earth did not do that; rather it brought forth trees yielding fruit but the trees themselves were not fruit.
Therefore, when Adam was punished for his sin, the land was punished too. As it says later on: ארורה האדמה בעבורך , accursed is the ground because of you.  

How are we to understand this? How could it be that the earth wouldn't listen to 'ה & bring forth trees the way He wanted?
Additionally, asks the חתם סופר,  why would 'ה wait until man sinned to punish the earth? Why wouldn't He punish it right away on the third day instead of waiting until day six?

The מהרי"ל דיסקין explains that the fact that the earth was able to alter what 'ה wanted teaches us that 'ה gave the land the right to choose; the land had the right to either listen to 'ה & bring out the trees the way He wanted or not. The land chose not to listen and was consequently punished.
What's the point in having creation able to go against His will?

From the start, Hashem was trying to teach us the power of free choice so He gave the land that choice. When it failed the test, He waited to see if Adam would learn from that & make the right choice to listen to 'ה . However, when Adam, too, failed, the land was punished along with Adam to teach this lesson for all time. We have the power to choose & will have to live with the choices we make.   

Hashem couldn't punish the land on day three when it sinned, because Adam wasn't created yet. The only reason  'ה punishes is to teach a lesson, so that one improves one’s ways. Therefore, until Adam was created, there was no one to learn the lesson. Punishing the land wouldn't accomplish anything; therefore Hashem waited for Adam to sin too, and then He punished them both together.

As we head into a new beginning, we must realize how important it is to make the right choices. 'ה trusts us & gives us free will; all we have to do is choose!