Well, of course Lincoln would dislike Jefferson. No surprises there.
Jefferson was a secessionist! (And, a successful one at that!)
And, Jefferson demolished Lincoln's justifications for making war on the southern states long before Lincoln even tried it: The Kentucky Resolves (1798?). The Kentucky Resolves were a response to the alien and sedition acts. Do take a moment to look it up and read the document. It provides an interesting analysis of the relationship between the state and the central government. Frequently cited is the 10th Amendment (power not delegated is reserved).