The South faced many problems during the Civil War, and it is easy to name three.
First, the South had the problem of having an agricultural economy. It is hard to win a war when all you produce is cotton, tobacco, and rice. The South had virtually no industrialization, and found it difficult to produce weapons or uniforms, for example. In spite of the fact that agricultural products can be turned into cash, plantations were not able to prosper because the plantation owners did not have enough manpower because of the disruptions of war and the enlisting of able men as soldiers. They could not produce enough to feed their slaves and make money. Some plantation owners enlisted themselves, and women were left to run the plantations. The women made a noble effort, but had insufficient resources to manage well.
A second problem the South had was that the war was mostly fought on in the South. A war that is fought on one's home ground is far more costly and painful than one fought on the ground of another. More civilians are sacrificed to the "cause," and the devastation and disruption are terrible.
A third problem for the South was organizational and political. The North had mechanisms in place with which to fight a war, with an established government and an established military. The South, while it was united on the matter of slavery, was not a cohesive country as the war began. It established a Confederacy and a military, but did not have the power of experience behind it.