It seems to me that a dispute arose over the meaning of the word "apostle." Paul is considered an apostle, but he is not one of the 12 Apostles. Peter, Andrew, James and John, Simon, James and Jude, Philip, Bartholomew, Matthew, Thomas and Matthias are the 12, and Paul is not among them. There were two "James": the Less and the Greater. Do you know why they were so called?
The Catholic Encyclopedia suggests that the nicknames refer to nothing more profound than the relative stature of the two apostles. If there's another theory, I'm not aware of it.