The correct answer to this open question is the following.
Jefferson noted that "All men are created equal" suggesting the this was "self-evident"
My opinion about what he meant with that quote is that he wanted to make a very clear statement on the issue that all men had natural rights that had to be respected. And the government should be the first institution to respect and protect American citizens.
The sorts of conflicts and misconceptions that may have stemmed from this statement were the particular interpretations that different factions and people made, according to their interests and agendas.