As Jefferson was the third President and the Federal Court system was designed to have life-time appointments, many of the original holders of Federal judicial posts were held by Federalist appointees who had not yet died in office or resigned.
So, Jefferson found himself waiting for turnover on the bench without much success.
Texas and mexico had a conflict because they couldn't decide who get to claim the Rio grande because the texas government wanted to claim it and mexico also wanted to so it became a dispute