There were many problems,
First, although they were technically 'free', there was little work in the war-tattered south, other than the very plantations from which these people were emancipated.
Secondly, they had no money or assets in most cases. Many began on the long migration of poor African Americans from the south to the industrial north, which continued through the 1970s.
The biggest problem, however, was the ongoing discrimination they faced. Jim Crow Laws throughout the south enforced segregation in public places, and most remained in place until the 1960s Civil Rights Movement ultimately resulted in Federal legislation negating most (unconstitutional) segregation laws.
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Answer:
They weren't treated like humans, but more as a commodity, something that can be used and abused without care. In the North, people were against slavery and working to end it, so naturally, you'd go somewhere safer, where you're actually seen as a human being with feelings and unalienable rights.