Final answer:
The domestic issues during Jefferson's presidency included political divisions due to Federalist judicial appointments by his predecessor Adams, policies toward Native Americans, and struggles to maintain U.S. neutrality during the Napoleonic Wars with acts like the Non-Intercourse Act.
Step-by-step explanation:
One significant domestic issue during the Jefferson presidency dealt with the political divisions stemming from President Adams's last-minute judicial appointments, which were largely Federalists. Thomas Jefferson, aligning with the Republican vision, opted not to deliver these commissions when he took office, reflecting the ongoing party tensions. Jefferson's presidency also saw a focus on policies related to Native Americans, including efforts to assimilate them into American agricultural life or pressuring them into debt to acquire their lands. Additionally, a major challenge for Jefferson was maintaining U.S. neutrality during the Napoleonic Wars, especially with the issues of British impressment of American sailors and the Non-Intercourse Act of 1808, which aimed to ease trade restrictions while still imposing embargoes on Britain and France.