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Adding to the above answer, Jefferson was accused by some with anti-federalist leanings of "Outfederalizing the Federalists" in that many of his actions as President seemed in direct contradiction to his strict constructionist principles.
For example, in addition to the Louisiana Purchase, he also constructed a temporary navy and went to war against the Barbary States in the Mediterranean. By sending Lewis and Clark all the way to the ocean, he established an American claim to the Pacific Northwest. Most troubling to small government proponents, he signed the Embargo Act in 1807, prohibiting American merchants from trading with anycountries involved in the Napoleonic Wars. This reminded people of the English Navigation Acts, and seemed like something distinctly un-Jeffersonian.
Lastly, as President he was an anti-federalist in charge of a federal government, an irony not lost on his former political enemy John Adams.
Jefferson's rule was filled with inconsistencies. They were not bad or inferior, but they were unique and represent a moment where pausing for analysis would be appropriate. The previous post did a very nice job in discussing Jefferson's challenges with slavery. One can find a similar element in his political affiliation. An avowed Republican, Jefferson believed that power should not rest in the elite powers located in the political discourse of Washington, D.C. Rather, he felt that the heart and soul of American politics lay in the agriculture base of America as well as the notion of "common people." At the same time, Jefferson was extremely bright, and received the finest of education, studying in France. This is not representative of the common citizenry of the time. A more nuanced complexity rests in his perception of government. Believing like most Republicans in the time of a small government that would not overstep its bounds, Jefferson went against this in the Louisiana Purchase, when Jefferson used the power of the Presidency to double the size of the United States. In the process, one could see that Jefferson might have tested his own principles in exceeding the reach of government and the presidency.
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.
He was inconsistent in terms of his political ideology, being a Federalist, and also, as pohnpei mentioned, he did not have a consistent definition of equality among all human beings.
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