@miayasmin
well at the heart of every conflict there are two or more different beliefs on the same issue
and there is no general belief more rigid, infallible and common than religion
so yeah religion, if applied too directly will always cause conflicts and within the setting of a manga where the hero is right and punishes the villain any religious organisation with a direct claim on worldly power will at least partly turn evil
in the real world those organisations have a ton of checks and balances to spot 9/10 problems early on and deal with them in-house but for a story that would make for a terrible plot.
its much easier, flashier and entertaining to have the hero/anti hero/ ml/mc blast those problems straight to hell after they have created a bit of drama/justification