One issue between the men was the Alien and Sedition Acts. Jefferson believed that the acts themselves leaned toward establishing a dictatorship, which was out of the question and against what they had fought for.
There was also Adam's last minute appointment of federal judges. This selection of "midnight judges" caused a huge rift between the two.
Thirdly, the Kentucky Resolution was supported by both Jefferson and Madison.
Jefferson commissioned the notorious scandalmonger, John Callender, to compose articles which ridiculed Adams both personally and politically. Jefferson’s association with Callender soon turned sour when Callender was arrested under the Alien and Sedition Acts for these articles. Callender, who believed Jefferson had under-paid him, published the story of Jefferson’s affair with his slave Sally Hemings."