What were three major issues of reconstruction?

-- What/how to do the Reconstruction. > How to bring the states back, what punishment - how severe/etc. 

-- What to do with the African Americans. > Lincoln only freed the Southern slaves with the Emancipation Proclamation, and it was only a formality. [The 13th, 14th and 15th Amendments show how the government dealt with this issue.] 

-- How to regulate that the Reconstruction was happening. The South was very belligerent about the Reconstruction - and made its own list of rules (aka Jim Crow Laws) to undermine the rights given to the African Americans by the amendments ^. 

I hope I helped a least a bit! :)