The Second Galactic Civil War was a total convoluted mess. Unlike the first Galactic Civil War, it didn't have two clear-cut sides, namely a rebellion completely made up of heroic idealists fighting on principle against a evil, oppressive empire. In fact, the roles were kind of switched around this time.
A variety of issues led to the Second Galactic Civil War, such as planets' rights, slavery, and differences on how to run the Galaxy. Eventually, the Corellian Confederation, led by the Five Worlds, seceded from the Galactic Federal Union That would have been simple enough, if the New Jedi Order and Wedge Antilles hadn't decided to kriff everything up by spontaneously changing sides before founding their own faction. The Hapes Consortium also helped with that.