Once the American Civil war ended, did some states encounter more difficulty than others when it came to rejoining the Union? What circumstances or conditions might have contributed to their issues?
The question refers to "problems" without defining them, so I am going to cast my answer in terms of which states rejoined the Union earlier (supposedly fewer "problems") rather than later. I will try to tie the rejoining order to the best correlation I can find.
According to the link below, Tennessee, Arkansas, North Carolina, and Florida were the first four Confederate states to rejoin the Union. They were Upper South (or in the case of Florida, peripheral) states that were not part of the mainstream South. The first three states plus Virginia did not join the Confederacy until after the firing on Fort Sumter.
The last seven states to rejoin were Louisiana, South Carolina, Alabama, Georgia, Virginia, Mississpi, and Texas. With the notable exception of Virginia, these were the hard core "deep South" states. The most pro-Union part of Virginia was West Virginia, which "seceded from secession," meaning that what was left was more pro South than the other Upper South states.