Basically, squabling over the location of the capitol city and state constitution.
Many persons wanted to divide the territory into northern and southern sections, each to become a state. Others favored the creation of a single state from the entire territory. In 1883 the territorial capital was moved from Yankton, in the southeastern corner, to Bismarck, in present North Dakota. This change caused many persons in the southern part to advocate the creation of South Dakota as a separate state.
On February 22, 1889, President Cleveland signed an act of Congress that divided the territory into two sections along a line just south of the 46th parallel. The act further authorized each section to set up a government in preparation for statehood. In South Dakota a constitution was adopted, Arthur C. Mellette was elected governor, and Pierre was chosen as the state capital. South Dakota was formally admitted to the Union on November 2, 1889.
The fall of the roman empire was because the territory that authorities had to govern was too large. When the United States were formed, north and south Carolina were spilt into 2 parts. When the Dakotas became states, they followed this same theory of 1 large state being too big to govern. Thats just my guess.