Is the baccalaureate certificate that I obtained from a private institution, which grants 25% of continuous assessment marks unjustly (undeservedly), considered unlawful (haram), and is it permissible to pursue university studies with this certificate?

If the education system allows for these points to be taken, then there is no harm. Otherwise, it is not permissible, and this should be clarified to the Ministry so that they may place you in the appropriate position for your grades and not advance you over someone who is more deserving than you, due to the generality of the Prophet's (peace be upon him) saying: "Whoever cheats is not of me."