If positive charges have higher electric potential difference than negative charges then why the negative charges (electrons) are the one that are moving in a circuit? and to my knowledge the direction of electric field from high EPD to low its just contradiction that electrons with low electric potential difference are moving?
This is where you have to be careful and realise that there is a difference between electric potential and electric potential energy.
Negatively charged electrons have a higher electric potential energy the lower (more negative) the potential becomes.
As one moves closer to a negatively changed object the lower (more negative) the electric potential becomes.
In order to move an electron closer to the negative charged object external work needs to be done and so the electric potential energy of the electron increases.
Release the electron and it will be repelled by the negatively charged object, gaining kinetic energy whilst losing electric potential energy.
Electrons flow naturally from a position of low potential to a position of higher potential.