Basically people in the North wanted all these new territories to be free and the people of the South wanted all of them to be slave states. This issue was solved in some way with the Missouri compromise of 1820, but years later some states broke this law such as in bleeding Kansas, where even though they were above the Missouri line they still had the possibility to be a slave state.
To sum it up, the controversy was on whether these territories would be free or slave states.
