I noticed when looking at the maps on this wikipedia page that often, when states were admitted, only a part of that territory became the actual state, and the remainder of the land was transferred to another territory or became unorganized. Why wouldn't the whole territory just become the new state?
If I understand your question correctly, the answer lies in the Northwest Ordinance. This early American legislation laid out the ways in which the Northwest Territory (modern-day Ohio, Indiana, Illinois, Michigan, and Wisconsin) would be divided into states. The ordinance lays out the step-by-step process which would dictate how this territory would be broken down. It traced the steps to sovereignty, beginning with a district being governed by U.S. appointed leaders, and ending with a territory being allowed to put its own leaders into place. While the actual admittance of states was laid out by the Enabling Act of 1802, the Northwest Ordinance laid out certain terms for the Northwest territory that served as precursors to their statedhood. For example, as stated in the fifth article of the Northwest Ordinance of 1787:
There shall be formed in the said territory, not less than three nor more than five states; and the boundaries of the states, as soon as Virginia shall alter her act of cession and consent to the same, shall become fixed and established as follows, to wit: The western state in the said territory, shall be bounded by the Missisippi, the Ohio and Wabash rivers;
Essentially, the ordinance says that there can be no less than 3 states and no more than 5 made out of the territory. It continues to lay out the boundaries of the future states. This is significant because about 1/3 of what would become Minnesota was in the Northwest territory, but I'd imagine they did not include it because it did not fall within the set boundaries and making it a separate state would exceed the five state maximum set by the ordinance. The document also discusses population as a determining factor in the sovereignty of territories.
I'm not sure if this completely addresses your question but either way, the Northwest Ordinance and the Enabling Acts that followed certainly helped to determine the ways in which the boundaries of states were formed by setting out calculated methods of how to fragment the territory.
Here is [a link to the actual text of the Northwest Ordinance of 1787](http://memory.loc.gov/cgi-bin/query/r?ammem/bdsdcc:@field(DOCID+@lit(bdsdcc22501) for further reading. Its a bit dense, but its an interesting read. I hope this helps to answer your question!
According to the book American Boundaries, new states-to-be often submitted to Congress larger areas than what would eventually become law. Congress would then often propose/suggest different, often smaller boundaries, and a back-and-forth debate might occur. Every state's creation was different, but it wasn't uncommon for a new state-to-be to desire a relatively large area and for Congress to desire a smaller area—this was quite common before the Civil War because if a free or slave territory could eventually be made into more rather than fewer states then the free or slave balance of power in Congress would end up more or less powerful.