in the book the Port to Chicago on page 38 Joe says, "we're supposed to be fighting the same enemy...I don't know who my enemy really is". What does he mean by this?

Edwards is referring to the racial segregation and prejudice. He'd just gone to a bar with two of his fellow servicemen and was refused service because of the color of his skin. All three men were serving their country, only one man was turned away, and in Edwards' eyes, he couldn't understand where the enemy truly was.... in another part of the world or in his own country.