The major inconsistency that one can see in President Jefferson is in his somewhat inconsistent attitude towards equality and liberty.
Jefferson, of course, was the man who wrote the Declaration of Independence. In it, he said that all men were created equal and he said that God had created them so.
However, his idea of the equality of all men did not extend to blacks. While he felt slavery was bad in many ways, he owned large numbers of slaves and (unlike George Washington) did not free them, even in his will.
It is, of course, inconsistent to argue on the one hand that British rule was unjust because all men are created equal while, at the same time, assuming that all blacks are inferior enough to enslave.