What are some complexities or any inconsistencies concerning President Thomas Jefferson?

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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...

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parama9000 | Student

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.