The article does a decent job talking about a few misconceptions. I'll parrot those and add some sources. Then I'll offer a few more.

The first misconception you always hear is that the war was over states rights. As the article points out, southerners actually were fighting against states rights. Northern liberty laws were erected so that northerners did not have to aid southern slave catchers who ventured into their regions looking for self-emancipated slaves. John C. Calhoun was perhaps the most articulate southerner on this point, advocating for a strong, centralized federal slave code that could be enforced from D.C. As you can imagine, that is pretty much the opposite of states rights'. Furthermore, the Dred Scott case effectively ruled out any ability to compromise on slavery, as it threw out the Missouri Compromise, the Compromise of 1850, and the Kansas-Nebraska Act and its accompanying notion of Popular Sovereignty. (Sources: William H. Freehling's Two Volumes, The Road to Disunion; Daniel Walker Howe's What Hath God Wrought, The Transformation of America, 1815-1848)

While many would argue that the war was not about slavery, Charles B. Dew's Apostles of Disunion: Southern Secession Commissioners and the Causes of the Civil War, uses the writings of various secession delegates to other states to prove that slavery was at the forefront of their decision to secede from the Union. These commissioners wrote at length about how white blood would be tainted by African Americans and used violent visuals of race war to convince other states that the Lincoln administration threatened not only slavery, but the white race as a whole. In years past, historians like Michael F. Holt in his work, The Political Crisis of the 1850s, argued that it was the break down of the two party system in the 1850s that led to secession. However, the nuance here was not to say that slavery wasn't an issue, his point was to ask why did a fight over slavery that had existed since the birth of this nation finally rupture in 1860? While he postulates some interesting positions, at the end of the day, slavery was the issue that cleaved the Union in twain.

Now for some lesser known misconceptions:

One such misconception describes the Civil War as the "rural agrarian South" vs. "the Industrialized North." Historians like Edward Ayers', Valley of the Shadow: Two Communities during the Civil War, argue that there were remarkable similarities between the two sections. While the North did contain more railroads, factories, and other industries than the South, the majority of the northern population still lived and worked on small farms. Part of this argument about similarities between sections seeks to question the debate about an "irrepressible conflict" between two divergent regions. Historians thus illustrate how in reality, the sections had numerous similarities that do not line up with the conception of mutually opposed civilizations of free labor and chattel slavery. Other historians like James Gigantino's The Ragged Road to Abolition, illustrates how slavery still existed in New Jersey and other northern states up till 1865. In fact, numerous slaves who had been given their "freedom" were still slaves in all but name. Furthermore, many of these freed people were sold South before their labor contracts expired. Steven Hahn's A Nation Under Their Feet and Slaves at Large, shows how slavery remained a national institution and should be thought of less a sectional difference than as a symbol of America's emergence into the modern nation-state that reimagined power relationships in this country. Lastly, Elliot West's article, Race and Reconstruction, argues that we need to abandon the North South binary and place the Civil War and Reconstruction in the context of the west. Here, we have some great evidence that, as Hahn suggested, the Civil War and Reconstruction and the emergence of the American West are emblematic of American sovereignty expanding over Natives, minorities, and the states. All had to become subject to the modern nation state and no competing sovereign entities could compete against that supremacy.

This is pretty long, I'll stop here. But for more misconceptions, ask away. I have ones on: some southerners supported enslaving poor whites, women and gender in the Civil War, the Civil War as a "low rape" war, and non-directly civil war related but still dealing with the legacies of reconstruction like the origins of segregation, the roles of disfranchisement and segregation, and whether Reconstruction was a success.