What were some major issues during the Reconstruction of the US?

One of the obvious ones, and this one lasted a long time, maybe even today is the Southerners gaining a hatred of the Northerners.

Union troops occupying the south, pissed many people off

Loss of slaves, production somewhat plummeted, due to Southerners needing to pay workers now.

Freed slaves moving to the North hoping to find better employment, this posed problems for the northerners, who felt threatened by the influx of freed slaves, and felt that they might lose their jobs to the freed slaves.

There are others, but I'm not American, so I can't tell you intimate details.