Now if you asked me how many churches there are supposed to be, I'd say one, if you mean capital "C" Church as in Body of Christ. If you mean small "c" church, as in congregations, well, the New Testament recognizes numerous churches.
I am referring to the church, the body of Christ. You are correct that there is only one body of Christ. You are also correct that there were numerous congregations of that body in the New Testament. The important thing to recognize is that they were all part of one body, and all were to be teaching the same thing. It is true that many of them dealt with problems of false teaching, and that is why Paul wrote to them to show them the error of their ways.