The major differences they had where: states rights, socioeconomic structure, and American foreign policy.
The question of strong individual states as opposed to a strong federal government sat at the heart of the founders’ disagreements, and caused discord among them. Within the young country, the Federalists desired a strong national government, whereas the Republicans did not. Republicans feared that a federal government could become too powerful, particularly in its ability to levy taxes, to raise standing armies, and to incur a national debt to foreign nations.