Magic may well have been real. Healing crystals, shamanry, witchcraft, voodoo, things of this nature may have been real at one point and have since been patched out. These could have simply been glitches in the program.
We’ve all heard of glitches in games that can be exploited that eventually get patched. Could have been real.
There’s a book series based on this general idea, it’s called Magic 2.0
That’s an excellent series by a pretty fun author. There’s an older example that I once read, but at the moment all I can remember is that the spells are calibrated to the exact physical state of the world at the time of casting (like that one xkcd comic). As a result, the protagonist foils enemy spells by doing things like causing worms to shift in the dirt or rocks to fall over.
Though the system doesn’t really hold up to scrutiny, I enjoyed the book. Hopefully someone remembers the premise and can tell me the title.
If you liked Magic 2.0, you would almost certainly enjoy the older YA series WebMage.
edit: Corrected auto correct.