The Proclamation applied in the ten states that were still in rebellion in 1863, and thus did not cover the nearly 500,000 slaves in the slave-holding border states (Missouri, Kentucky, Maryland or Delaware) that had not seceded. Those slaves were freed by later separate state and federal actions.
The Jim Crow laws supported the mistreatment
The Federal Government of the United States is the national government of the United States, a federal republic in North America, composed of 50 states, a federal district, five major self-governing territories, and several island possessions
A state government is the government of a country subdivision in a federal form of government, which shares political power with the federal or national government. A state government may have some level of political autonomy, or be subject to the direct control of the federal government.